Compositions comprising thienopyrimidine and thienopyridine compounds and methods of use thereof

ABSTRACT

The present disclosure relates generally to thienopyrimidine and thienopyridine compounds and methods of use thereof. In particular embodiments, the present disclosure provides compositions comprising thienopyrimidine and thienopyridine compounds of Formula 4b: 
                         
and methods of use to inhibit the interaction of menin with MLL1, MLL2 and MLL-fusion oncoproteins.

The present application is the National Stage of International Application No. PCT/US2014/022750, filed Mar. 10, 2014, which claims priority to U.S. Provisional Patent Application Ser. No. 61/780,099, filed Mar. 13, 2013, the entire disclosures of which are herein incorporated by reference in their entireties.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made with government support under R01 CA160467-01 awarded by the National Institutes of Health. The government has certain rights in the invention.

FIELD OF THE INVENTION

The present invention relates generally to thienopyrimidine and thienopyridine class compounds and methods of use thereof. In particular embodiments, the present invention provides compositions comprising thienopyrimidine and thienopyridine class compounds and methods of use to inhibit the interaction of menin with MLL1, MLL2 and MLL-fusion oncoproteins (e.g., for the treatment of leukemia, solid cancers and other diseases dependent on activity of MLL1, MLL2, MLL fusion proteins, and/or menin).

BACKGROUND OF THE INVENTION

Chromosomal translocations that affect the proto-oncogene Mixed Lineage Leukemia (MLL) occur in aggressive human acute leukemias, both in children and adults (Sorensen et al., J Clin Invest., 1994.93(1): p. 429-37, Cox, et al., Am J Clin Pathol., 2004. 122(2): p. 298-306, herein incorporated by reference in their entireties). They are particularly common in infants with acute myeloblastic leukemia (AML) and acute lymphoblastic leukemia (ALL) and constitute up to 80% of all infant acute leukemia cases. Fusion of MLL with one of 60 partner genes forms a chimeric oncogene which upregulates HOX genes resulting in a blockage of blood cell differentiation that ultimately leads to acute leukemia (Eguchi et al. Int J Hematol., 2003. 78(5): p. 390-401, herein incorporated by reference in its entirety). Patients with leukemias harboring MLL translocations have a very poor prognosis (35% five year survival) and it is clear that novel therapeutic strategies are urgently needed to treat these leukemias (Slany. Hematol OncoI., 2005. 23(1): p. 1-9, herein incorporated by reference in its entirety). Menin is a critical cofactor in MLL-associated leukemias. Menin is a tumor-suppressor protein encoded by the Multiple Endocrine Neoplasia (MEN) gene. Menin is a ubiquitously expressed nuclear protein that is engaged in interactions with a cohort of transcription factors, chromatin modifying proteins, and DNA processing and repair proteins (Agarwal et al. Horm Metab Res., 2005. 37(6): p. 369-74, herein incorporated by reference in its entirety). The biological function of menin remains unclear and is context dependent. It functions as a tumor suppressor in endocrine organs (Marx. Nat Rev Cancer., 2005. 5(5): p. 367-75, herein incorporated by reference in its entirety) but has an oncogenic role in myeloid cells (Yokoyama et al., Cell., 2005. 123(2): p. 207-18, herein incorporated by reference in its entirety). Association of menin with oncogenic MLL fusion proteins constitutively up-regulates expression of HOX genes and impairs proliferation and differentiation of hematopoietic cells leading to leukemia development. Myeloid cells transformed with oncogenic MLL-AF9 fusion protein require menin for efficient proliferation (Chen et al., Proc Natl Acad Sci USA., 2006. 103(4): p. 1018-23, herein incorporated by reference in its entirety). Menin is also required to maintain oncogenic transformation induced by other MLL translocations, including MLL-ENL, MLL-GAS7 and MLL-AF6 (Yokoyama et al., Cell., 2005.123(2): p. 207-18, herein incorporated by reference in its entirety), demonstrating that menin functions as a general oncogenic cofactor in MLL-related leukemias and implies the interaction of menin with MLL fusions and MLL is a valuable target for molecular therapy. The leukemogenic activity of MLL fusion oncoproteins is dependent on association with menin. Therefore, selective targeting of this interaction could provide an attractive therapeutic approach to develop novel drugs for leukemias with translocations of MLL gene and other leukemias with upregulation of HOX genes.

SUMMARY OF THE INVENTION

In some embodiments, the present invention provides compositions for the treatment of leukemia which inhibit binding of one or more MLL fusion proteins to menin and/or MLL wild type to menin. In some embodiments, the composition comprises a thienopyrimidine and thienopyridine class compounds.

In some embodiments, the thienopyrimidine and thienopyridine class compound is of the general formula:

wherein X, Y, W, R1, R2, R3, and R4 are independently selected from any of the respective substituents described herein or depicted in any of Tables 1-8 or described elsewhere herein, in any combination. For example, in some embodiments, R₁-R₄ each independently consist of or comprise: H, alkyl group (e.g., straight-chain alkyl (e.g., methane, ethane, propane, butane, pentane, hexane, etc.), branched alkyl group (e.g., iso-propane, 2-methyl-hexane, 3-methyl,2-propyl-octane, etc.), cycloalkyl (e.g., cyclopropane, cyclobutane, cyclopentane, cyclohexane, cyclooctane, etc.), branched cyclic alkyl (e.g., methylcyclohexane, ethylcyclobutane, propylcyclohexane, etc.)), a substituted alkyl group (e.g., halogen-substituted alkyl group (e.g., mono-, di-, tetra-,penta- and trihaloethane (e.g., trifluoroethane), halomethane (e.g., fluoromethane), dihalomethane (e.g., difluoromethane), trihalomethane (e.g., trifluoromethane), etc.), alkycyano (e.g., cyano, methylcyano, ethylcyano, etc.), alkoxy group (e.g., ether, alcohol, etc.), alkylamine (e.g., primary amine (e.g., ethylamine, iso-butylamine, n-propylamine, sec-butylamine, iso-propylamine, iso-amylamine, methylamine, dimethylamine, n-amylamine, etc.), secondary amines (e.g., dimethylamine, methylethanolamine, diphenylamine, etc.), tertiary amine (e.g., trimethylamine, triphenylamine, etc.), thioalkyl, combinations thereof, etc.), a substituted cycloalkyl group (e.g., halogen-substituted cycloalkyl group, alkyl-substituted cycloalkyl group, cycloalkoxy group, cyclolkylamine, etc.), a halogen (e.g., F, Cl, Br, I, and At), a ketone, a carbocyclic ring, an aromatic ring (e.g., heteroaryl), a substituted aromatic ring (e.g., branched aromatic ring (e.g., ethylbenzene, methyl benzene, etc.), halobenzene (e.g., chlorobenzene, fluorobenzene, etc.)), a heterocyclic aromatic ring (e.g., comprising one or more nitrogen, oxygen and/or sulfur members which may be non-substituted or substituted with alkyl, aryl, halogen, hydrogen bond donor or acceptor), a heterocyclic non-aromatic ring (e.g., comprising carbon and one or more nitrogen, oxygen and/or sulfur members), carbocyclic or heterocyclic aromatic ring comprising carbon atoms and one or more nitrogen, oxygen and/or sulfur members fused to another aromatic ring (e.g., heteroaryl), a multi-ring system comprising a combination of elements selected from aromatic rings, cycloalkane, heterocyclic rings, alkyl chains, and suitable C-, N-, O-, S-, and/or halogen-containing substituents (e.g., substituted heteroaryl), or a hydrogen bond donor or a hydrogen bond acceptor, and/or combinations thereof.

In some embodiments, the thienopyrimidine and thienopyridine class compound is of a general formula of:

wherein R1 and R2 both independently comprise or consists of: H, alkyl group (e.g., straight-chain alkyl (e.g., methane, ethane, propane, butane, pentane, hexane, etc.), branched alkyl group (e.g., iso-propane, 2-methyl-hexane, 3-methyl,2-propyl-octane, etc.), cycloalkyl (e.g., cyclopropane, cyclobutane, cyclopentane, cyclohexane, cyclooctane, etc.), branched cyclic alkyl (e.g., methylcyclohexane, ethylcyclobutane, propylcyclohexane, etc.)), a substituted alkyl group (e.g., halogen-substituted alkyl group (e.g., mono-, di-, tetra-,penta- and trihaloethane (e.g., trifluoroethane), halomethane (e.g., fluoromethane), dihalomethane (e.g., difluoromethane), trihalomethane (e.g., trifluoromethane), 1-trihalo, 2-halo-ethane, trihalobutane, etc.), alkoxy group (e.g., ether, alcohol, etc.), alkylamine (e.g., primary amine (e.g., ethylamine, iso-butylamine, n-propylamine, sec-butylamine, iso-propylamine, iso-amylamine, methylamine, dimethylamine, n-amylamine, etc.), secondary amines (e.g., dimethylamine, methylethanolamine, diphenylamine, etc.), tertiary amine (e.g., trimethylamine, triphenylamine, etc.), thioalkyl, combinations thereof, etc.), a substituted cycloalkyl group (e.g., halogen-substituted cycloalkyl group, alkyl-substituted cycloalkyl group, cycloalkoxy group, cyclolkylamine, etc.), a halogen (e.g., F, Cl, Br, I, and At), a ketone, a carbocyclic ring, an aromatic ring (e.g., heteroaryl), a substituted aromatic ring (e.g., branched aromatic ring (e.g., ethylbenzene, methyl benzene, etc.), halobenzene (e.g., chlorobenzene, fluorobenzene, etc.)), a heterocyclic aromatic ring (e.g., comprising one or more nitrogen, oxygen and/or sulfur members which may be non-substituted or substituted with alkyl, aryl, halogen, hydrogen bond donor or acceptor), a heterocyclic non-aromatic ring (e.g., comprising carbon and one or more nitrogen, oxygen and/or sulfur members), carbocyclic or heterocyclic aromatic ring comprising carbon atoms and one or more nitrogen, oxygen and/or sulfur members fused to another aromatic ring (e.g., heteroaryl), a multi-ring system comprising a combination of elements selected from aromatic rings, cycloalkane, heterocyclic rings, alkyl chains, and suitable C-, N-, O-, S-, and/or halogen-containing substituents (e.g., substituted heteroaryl), or a hydrogen bond donor or a hydrogen bond acceptor, and/or combinations thereof; and wherein A, B, and D each independently comprise or consist of: C, N, O, or S; wherein when one or more of A, B, and/or D comprise O or S, there is no further substitution at that respective position; wherein when one or more of A, B, and/or D comprise N or C that respective position is optionally substituted, wherein the substituent at that respective position comprises or consists of: alkyl group (e.g., straight-chain alkyl (e.g., methane, ethane, propane, butane, pentane, hexane, etc.), branched alkyl group (e.g., iso-propane, 2-methyl-hexane, 3-methyl,2-propyl-octane, etc.), cycloalkyl (e.g., cyclopropane, cyclobutane, cyclopentane, cyclohexane, cyclooctane, etc.), branched cyclic alkyl (e.g., methylcyclohexane, ethylcyclobutane, propylcyclohexane, etc.)), a substituted alkyl group (e.g., halogen-substituted alkyl group (e.g., trihaloethane (e.g., trifluoroethane), halomethane (e.g., fluoromethane), dihalomethane (e.g., difluoromethane), trihalomethane (e.g., trifluoromethane), etc.), alkoxy group (e.g., ether, alcohol, etc.), alkylamine (e.g., primary amine (e.g., ethylamine, iso-butylamine, n-propylamine, sec-butylamine, iso-propylamine, iso-amylamine, methylamine, dimethylamine, n-amylamine, etc.), secondary amines (e.g., dimethylamine, methylethanolamine, diphenylamine, etc.), tertiary amine (e.g., trimethylamine, triphenylamine, etc.), thioalkyl, combinations thereof, etc.), a substituted cycloalkyl group (e.g., halogen-substituted cycloalkyl group, cycloalkoxy group, cycloalkylamine, etc.), a halogen (e.g., F, Cl, Br, I, and At), a ketone, a carbocyclic ring, an aromatic ring, a substituted aromatic ring (e.g., branched aromatic ring (e.g., ethylbenzene, methyl benzene, etc.), halobenzene (e.g., chlorobenzene, fluorobenzene, etc.)), a heterocyclic aromatic ring (e.g., comprising one or more nitrogen, oxygen and/or sulfur members which may be non-substituted or substituted with alkyl, aryl, halogen, hydrogen bond donor or acceptor, a heterocyclic non-aromatic ring (e.g., comprising carbon and one or more nitrogen, oxygen and/or sulfur members), carbocyclic or heterocyclic aromatic ring (e.g., heteroaryl) comprising carbon atoms and one or more nitrogen, oxygen and/or sulfur members fused to another aromatic ring, a multi-ring system comprising a combination of elements selected from aromatic rings (e.g., heteroaryl), cycloalkane, heterocyclic rings, alkyl chains, and suitable C-, N-, O-, S-, and/or halogen-containing substituents, or a hydrogen bond donor or a hydrogen bond acceptor, and/or combinations thereof; and wherein Y is N or C, and wherein when Y is C the Y position may be substituted with R^(a), with R^(a) consisting of or comprising an H, alkyl (e.g., branched (e.g., isopropyl), straight chain (e.g., propyl), cycloalkyl (e.g., cyclopropyl)), heteroalkyl (e.g., methyl propyl ether), alkyl-substituted aryl (e.g., ethylbenzene), substituted alkyl (e.g., halo-substituted alkyl (e.g., trihalomethyl group (e.g., trifluoromethyl group), monohaloalkyl group (e.g. monofluoroethyl group), dihaloalkyl group (e.g. difluoroethyl group), trihaloethyl group (e.g., trifluoroethyl group), trihalopropyl (e.g., trifluoropropyl ((CH₂)₂CF₃), trihalobutyl group (e.g., trifluorobutyl group ((CH₂)₃CF₃)), 1-trifluoro,2-ethanol, alcohol (e.g., (CH₂)_(n)OH, wherein n=0-10), alkoxy (e.g., (CH₂)_(n)—OR, wherein n=0-10, wherein R is alkyl, (CH₂)_(n)-aryl, (CH₂)_(n)-aromatic, (CH₂)_(n)-heterocycle, substituted or non-substituted aryl, aromatic or non-aromatic heterocycle with one or more N, S, O, etc.), amino (e.g., alkyl amine, amino alkyl, etc.), cyano, sulfonyl, methoxy, aldehyde, heterocycle, aromatic, combinations thereof, etc.; and wherein L is present or absent and comprises alkylene (e.g. methylene, —CH₂—, ethylene, —CH₂—CH₂—, etc) or oxalkylene (e.g. —O—, —CH₂—O—CH₂) groups.

In some embodiments, R1 of subscaffold 1 is selected from an alkyl (e.g., branched (e.g., isopropyl), straight chain (e.g., propyl), cycloalkyl (e.g., cyclopropyl)), heteroalkyl (e.g., methyl propyl ether), alkyl-substituted aryl (e.g., ethylbenzene), substituted alkyl (e.g., halo-substituted alkyl (e.g., trihalomethyl group (e.g., trifluoromethyl group), monohaloalkyl group (e.g. monofluoroethyl group), dihaloalkyl group (e.g. difluoroethyl group), trihaloethyl group (e.g., trifluoroethyl group, See, e.g., compound 1), trihalopropyl (e.g., trifluoropropyl ((CH₂)₂CF₃), trihalobutyl group (e.g., trifluorobutyl group ((CH₂)₃CF₃)), trihaloisopropyl (e.g., trifluoroisopropyl (See, e.g., compound 38)), 1-fluoro,2-trifluoro, ethane (See, e.g., compound 21), 1-trifluoro,2-ethanol (See, e.g., compound 23)), alcohol, amino (e.g., alkyl amine, amino alkyl, etc.), cyano, sulfonyl, methoxy, aldehyde, heterocycle, aromatic, combinations thereof, etc.

In some embodiments, R2 of subscaffold 1 is selected from a halogen (e.g., Cl, F, Br, I), alkyl (e.g., branched, straight chain (e.g., methyl), cycloalkyl, heteroalkyl, alkyl-substituted aryl, substituted alkyl (e.g., halo-substituted alkyl, alcohol, amino, etc.), OH, SH, NH₂, etc.

In some embodiments, A of subscaffold 1 is selected from C, N, O, or S; wherein when A is O or S, there is no further substitution at that respective position; wherein, when A is N, it is optionally substituted with one substituent that comprises or consists of: alkyl (e.g., branched (e.g., isopropyl), straight chain (e.g., methyl, propyl), cycloalkyl (e.g., cyclopropane, cyclopentante, cyclohexane)), heteroalkyl (e.g., methyl propyl ether (CH₂O(CH2)₂CH₃), methylamine (CH₂NH₂), aminomethyl (CH₂NH), etc.), alkyl-substituted aryl (e.g., methylbenzene, ethylbenzene, propylbenzene, butylbenzene, etc.), substituted alkyl (e.g., halo-substituted alkyl (e.g., trihalomethyl group (e.g., trifluoromethyl group), trihaloethyl group (e.g., trifluoroethyl group), trihalopropyl (e.g., trifluoropropyl), trihalobutyl group (e.g., trifluorobutyl group), trihaloisopropyl(e.g., trifluoroisopropyl), 1-fluoro,2-trifluoro, ethane, trifluoroethanol), alcohol-substituted alkyl, amino-substituted alkyl, substituted cycloalkyl, substituted aromatic ring (e.g., propylbenzene, 1-ethyl-4methoxybenzene, 1-propyl-4-methoxy-benzene, etc.)), alcohol, amino, and/or combinations thereof; wherein when A is C, it is optionally substituted with one or two substituents that comprises or consists of: alkyl (e.g., branched (e.g., isopropyl), straight chain (e.g., methyl, propyl), cycloalkyl (e.g., cyclopropane, cyclopentante, cyclohexane)), heteroalkyl (e.g., methyl propyl ether, methylamino, etc.), alkyl-substituted aryl (e.g., methylbenzene, ethylbenzene, propylbenzene, butylbenzene, etc.), substituted alkyl (e.g., halo-substituted alkyl (e.g., trihalomethyl group (e.g., trifluoromethyl group), trihaloethyl group (e.g., trifluoroethyl group), trihalopropyl (e.g., trifluoropropyl), trihalobutyl group (e.g., trifluorobutyl group), trihaloisopropyl (e.g., trifluoroisopropyl), 1-fluoro,2-trifluoro, ethane, trifluoroethanol), alcohol-substituted alkyl, amino-substituted alkyl, substituted cycloalkyl, substituted aromatic ring (e.g., propylbenzene, 1-ethyl-4methoxybenzene, 1-propyl-4-methoxy-benzene, etc.)), alcohol, amino, and/or combinations thereof.

In some embodiments, B of subscaffold 1 is selected from C, N, O, or S; wherein when B is O or S, there is no further substitution at that respective position; wherein, when B is N, it is optionally substituted with one substituent that comprises or consists of: alkyl (e.g., branched (e.g., isopropyl), straight chain (e.g., methyl, propyl), cycloalkyl (e.g., cyclopropane, cyclopentante, cyclohexane)), heteroalkyl (e.g., methyl propyl ether, methylamino, etc.), alkyl-substituted aryl (e.g., methylbenzene, ethylbenzene, propylbenzene, butylbenzene, etc.), substituted alkyl (e.g., halo-substituted alkyl (e.g., trihalomethyl group (e.g., trifluoromethyl group), trihaloethyl group (e.g., trifluoroethyl group), trihalopropyl (e.g., trifluoropropyl), trihalobutyl group (e.g., trifluorobutyl group), trihaloisopropyl (e.g., trifluoroisopropyl), 1-fluoro,2-trifluoro, ethane, trifluoroethanol), alcohol-substituted alkyl, amino-substituted alkyl, substituted cycloalkyl, substituted aromatic ring (e.g., propylbenzene, 1-ethyl-4-methoxybenzene, 1-propyl-4-methoxy-benzene, alcohol, amino, and/or combinations thereof; wherein when B is C, it is optionally substituted with one or two substituents that comprises or consists of: alkyl (e.g., branched (e.g., isopropyl), straight chain (e.g., methyl, propyl), cycloalkyl (e.g., cyclopropane, cyclopentante, cyclohexane)), alkyl-substituted cycloalkyl (e.g. methylcyclohexyl), heteroalkyl (e.g., methyl propyl ether, methylamino, etc.), alkyl-substituted aryl (e.g., methylbenzene, ethylbenzene, propylbenzene, butylbenzene, etc.), substituted alkyl (e.g., halo-substituted alkyl (e.g., trihalomethyl group (e.g., trifluoromethyl group), dihalomethyl group (e.g. difluoromethyl group), monohalomethyl group (3.g. monofluoromethyl group)), trihaloethyl group (e.g., trifluoroethyl group), trihalopropyl (e.g., trifluoropropyl), trihalobutyl group (e.g., trifluorobutyl group), trihaloisopropyl (e.g., trifluoroisopropyl), 1-fluoro,2-trifluoro, ethane (See, e.g., compound 21), trifluoroethanol), alcohol-substituted alkyl, amino-substituted alkyl, substituted cycloalkyl, substituted aromatic ring (e.g., propylbenzene, 1-ethyl-4methoxybenzene, 1-propyl-4-methoxy-benzene, etc.)), alcohol, amino, and/or combinations thereof (See, e.g., Table 1).

In some embodiments, D of subscaffold 1 is selected from C, N, O, or S; wherein when D is O or S, there is no further substitution at that respective position; wherein, when D is N, it is optionally substituted with one substituent that comprises or consists of: alkyl (e.g., branched (e.g., isopropyl), straight chain (e.g., methyl, propyl), cycloalkyl (e.g., cyclopropane, cyclopentante, cyclohexane)), heteroalkyl (e.g., methyl propyl ether, methylamino, etc.), alkyl-substituted aryl (e.g., methylbenzene, ethylbenzene, propylbenzene, butylbenzene, etc.), substituted alkyl (e.g., halo-substituted alkyl (e.g., trihalomethyl group (e.g., trifluoromethyl group), trihaloethyl group (e.g., trifluoroethyl group), trihalopropyl (e.g., trifluoropropyl), trihalobutyl group (e.g., trifluorobutyl group), trihaloisopropyl (e.g., trifluoroisopropyl), 1-fluoro,2-trifluoro, ethane, trifluoroethanol), alcohol-substituted alkyl, amino-substituted alkyl, substituted cycloalkyl, substituted aromatic ring (e.g., propylbenzene, 1-ethyl-4methoxybenzene, 1-propyl-4-methoxy-benzene, etc.)), alcohol, amino, and/or combinations thereof; wherein when D is C, it is optionally substituted with one or two substituents that comprises or consists of: alkyl (e.g., branched (e.g., isopropyl), straight chain (e.g., methyl, propyl), cycloalkyl (e.g., cyclopropane, cyclopentante, cyclohexane)), heteroalkyl (e.g., methyl propyl ether, methylamino, etc.), alkyl-substituted aryl (e.g., methylbenzene, ethylbenzene, propylbenzene, butylbenzene, etc.), substituted alkyl (e.g., halo-substituted alkyl (e.g., trihalomethyl group (e.g., trifluoromethyl group), trihaloethyl group (e.g., trifluoroethyl group), trihalopropyl (e.g., trifluoropropyl), trihalobutyl group (e.g., trifluorobutyl group), trihaloisopropyl (e.g., trifluoroisopropyl), 1-fluoro,2-trifluoro, ethane, trifluoroethanol), alcohol-substituted alkyl, amino-substituted alkyl, substituted cycloalkyl, substituted aromatic ring (e.g., propylbenzene, 1-ethyl-4methoxybenzene, 1-propyl-4-methoxy-benzene, etc.)), alcohol, amino, and/or combinations thereof (See, e.g., Table 1).

In some embodiments, Y of subscaffold 1 is selected from N or C.

In some embodiments, L of subscaffold 1 is alkylene (e.g. methylene, —CH₂—, ethylene, —CH₂—CH₂—, etc) or oxalkylene (e.g. —O—, —CH₂—O—CH₂) groups.

In some embodiments, compositions comprising one or more of compound 1-42 of Table 1 are provided.

In some embodiments, the thienopyrimidine class compound is of a general formula of:

wherein R1 and R2 both independently comprise or consist of: H, alkyl group (e.g., straight-chain alkyl (e.g., methane, ethane, propane, butane, pentane, hexane, etc.), branched alkyl group (e.g., iso-propane, 2-methyl-hexane, 3-methyl,2-propyl-octane, etc.), cycloalkyl (e.g., cyclopropane, cyclobutane, cyclopentane, cyclohexane, cyclooctane, etc.), branched cyclic alkyl (e.g., methylcyclohexane, ethylcyclobutane, propylcyclohexane, etc.)), a substituted alkyl group (e.g., halogen-substituted alkyl group (e.g., mono-, di-, tetra-,penta- and trihaloethane (e.g., trifluoroethane), halomethane (e.g., fluoromethane), dihalomethane (e.g., difluoromethane), trihalomethane (e.g., trifluoromethane), etc.), alkoxy group (e.g., ether, alcohol, etc.), alkylamine (e.g., primary amine (e.g., ethylamine, iso-butylamine, n-propylamine, sec-butylamine, iso-propylamine, iso-amylamine, methylamine, dimethylamine, n-amylamine, etc.), secondary amines (e.g., dimethylamine, methylethanolamine, diphenylamine, etc.), tertiary amine (e.g., trimethylamine, triphenylamine, etc.), thioalkyl, combinations thereof, etc.), a substituted cycloalkyl group (e.g., halogen-substituted cycloalkyl group, cycloalkoxy group, cycloalkylamine, etc.), a halogen (e.g., F, Cl, Br, I, and At), a ketone, a carbocyclic ring, an aromatic ring, a substituted aromatic ring (e.g., branched aromatic ring (e.g., ethylbenzene, methyl benzene, etc.), halobenzene (e.g., chlorobenzene, fluorobenzene, etc.)), a heterocyclic aromatic ring (e.g., comprising one or more nitrogen, oxygen and/or sulfur members which may be non-substituted or substituted with alkyl, aryl, halogen, hydrogen bond donor or acceptor), a heterocyclic non-aromatic ring (e.g., comprising carbon and one or more nitrogen, oxygen and/or sulfur members), carbocyclic or heterocyclic aromatic ring comprising carbon atoms and one or more nitrogen, oxygen and/or sulfur members fused to another aromatic ring, a multi-ring system comprising a combination of elements selected from aromatic rings, cycloalkane, heterocyclic rings, alkyl chains, and suitable C-, N-, O-, S-, and/or halogen-containing substituents, or a hydrogen bond donor or a hydrogen bond acceptor, and/or combinations thereof; wherein R3 comprises or consists of: H, alkyl group (e.g., straight-chain alkyl (e.g., methane, ethane, propane, butane, pentane, hexane, etc.), branched alkyl group (e.g., iso-propane, 2-methyl-hexane, 3-methyl,2-propyl-octane, etc.), cycloalkyl (e.g., cyclopropane, cyclobutane, cyclopentane, cyclohexane, cyclooctane, etc.), branched cyclic alkyl (e.g., methylcyclohexane, ethylcyclobutane, propylcyclohexane, etc.)), a substituted alkyl group (e.g., halogen-substituted alkyl group (e.g., trihaloethane (e.g., trifluoroethane), halomethane (e.g., fluoromethane), dihalomethane (e.g., difluoromethane), trihalomethane (e.g., trifluoromethane), etc.), alkoxy group (e.g., ether, alcohol, etc.), alkylamine (e.g., primary amine (e.g., ethylamine, iso-butylamine, n-propylamine, sec-butylamine, iso-propylamine, iso-amylamine, methylamine, dimethylamine, n-amylamine, etc.), secondary amines (e.g., dimethylamine, methylethanolamine, diphenylamine, etc.), tertiary amine (e.g., trimethylamine, triphenylamine, etc.), thioalkyl, combinations thereof, etc.), a substituted cycloalkyl group (e.g., halogen-substituted cycloalkyl group, cycloalkoxy group, cycloalkylamine, etc.), a halogen (e.g., F, Cl, Br, I, and At), a ketone, a carbocyclic ring, an aromatic ring, a substituted aromatic ring (e.g., branched aromatic ring (e.g., ethylbenzene, methyl benzene, etc.), halobenzene (e.g., chlorobenzene, fluorobenzene, etc.)), a heterocyclic aromatic ring (e.g., comprising one or more nitrogen, oxygen and/or sulfur members which may be non-substituted or substituted with alkyl, aryl, halogen, hydrogen bond donor or acceptor), a heterocyclic non-aromatic ring (e.g., comprising carbon and one or more nitrogen, oxygen and/or sulfur members), carbocyclic or heterocyclic aromatic ring comprising carbon atoms and one or more nitrogen, oxygen and/or sulfur members fused to another aromatic ring, a multi-ring system comprising a combination of elements selected from aromatic rings, cycloalkane, heterocyclic rings, alkyl chains, and suitable C-, N-, O-, S-, and/or halogen-containing substituents, a hydrogen bond donor or a hydrogen bond acceptor, a sulfur-containing group (e.g., thiol, sulfide, disulfide, sulfoxide, sulfone (e.g., dimethyl sulfone, sulfonyl-amino (SO₂NH₂), sulfonyl-methane (SO₂CH₃), amino-sulfonyl-methane (NHSO₂CH₃), amino-sulfonyl-amino (NHSO₂NH₂), methy-sulfonyl-amino (CH₂SO₂NH₂; See, e.g. compound 96), methyl-sulfonyl-methane (CH₂SO₂CH₃), methyl-sulfonyl-halomethane (CH₂SO₂CH₃)) and/or combinations thereof; wherein R3 is present at 1-4 positions on the phenyl ring; wherein L is present or absent and comprises alkylene (e.g. methylene, —CH₂—, ethylene, —CH₂—CH₂—, etc) or oxalkylene (e.g. —O—, —CH₂—O—CH₂) groups; wherein Q comprises alkyl (C₁₋₅) or heteroalkyl with one or more N, O atoms; wherein Y is N or C, and wherein when Y is C the Y position may be substituted with R^(a), with R^(a) consisting of or comprising an alkyl (e.g., branched (e.g., isopropyl), straight chain (e.g., propyl), cycloalkyl (e.g., cyclopropyl)), heteroalkyl (e.g., methyl propyl ether), alkyl-substituted aryl (e.g., ethylbenzene), substituted alkyl (e.g., halo-substituted alkyl (e.g., trihalomethyl group (e.g., trifluoromethyl group), monohaloalkyl group (e.g. monofluoroethyl group), dihaloalkyl group (e.g. difluoroethyl group), trihaloethyl group (e.g., trifluoroethyl group), trihalopropyl (e.g., trifluoropropyl ((CH₂)₂CF₃), trihalobutyl group (e.g., trifluorobutyl group ((CH₂)₃CF₃)), trihaloisopropyl (e.g., trifluoroisopropyl, 1-fluoro,2-trifluoro, ethane, 1-trifluoro,2-ethanol, alcohol (e.g., (CH₂)_(n)OH, wherein n=0-10), alkoxy (e.g., (CH₂)_(n)—OR, wherein n=0-10, wherein R is alkyl, (CH₂)_(n)-aryl, (CH₂)_(n)-aromatic, (CH₂)_(n)-heterocycle, substituted or non-substituted aryl, aromatic or non-aromatic heterocycle with one or more N, S, O, etc.), amino (e.g., alkyl amine, amino alkyl, etc.), cyano, sulfonyl, methoxy, aldehyde, heterocycle, aromatic, combinations thereof, etc.; wherein Z comprises or consists of: H, alkyl group (e.g., straight-chain alkyl (e.g., methane, ethane, propane, butane, pentane, hexane, etc.), branched alkyl group (e.g., iso-propane, 2-methyl-hexane, 3-methyl,2-propyl-octane, etc.), cycloalkyl (e.g., cyclopropane, cyclobutane, cyclopentane, cyclohexane, cyclooctane, etc.), branched cyclic alkyl (e.g., methylcyclohexane, ethylcyclobutane, propylcyclohexane, etc.)), a substituted alkyl group (e.g., halogen-substituted alkyl group (e.g., trihaloethane (e.g., trifluoroethane), halomethane (e.g., fluoromethane), dihalomethane (e.g., difluoromethane), trihalomethane (e.g., trifluoromethane), etc.), alkoxy group (e.g., ether, alcohol, etc.), alkylamine (e.g., primary amine (e.g., ethylamine, iso-butylamine, n-propylamine, sec-butylamine, iso-propylamine, iso-amylamine, methylamine, dimethylamine, n-amylamine, etc.), secondary amines (e.g., dimethylamine, methylethanolamine, diphenylamine, etc.), tertiary amine (e.g., trimethylamine, triphenylamine, etc.), thioalkyl, a substituted cycloalkyl group (e.g., halogen-substituted cycloalkyl group, cycloalkoxy group, cycloalkylamine, etc.), a halogen (e.g., F, Cl, Br, I, and At), a ketone, a carbocyclic ring, an aromatic ring, a substituted aromatic ring (e.g., branched aromatic ring (e.g., ethylbenzene, methyl benzene, etc.), halobenzene (e.g., chlorobenzene, fluorobenzene, etc.)), a heterocyclic aromatic ring (e.g., comprising one or more nitrogen, oxygen and/or sulfur members which may be non-substituted or substituted with alkyl, aryl, halogen, hydrogen bond donor or acceptor), a heterocyclic non-aromatic ring (e.g., comprising carbon and one or more nitrogen, oxygen and/or sulfur members), carbocyclic or heterocyclic aromatic ring comprising carbon atoms and one or more nitrogen, oxygen and/or sulfur members fused to another aromatic ring, a multi-ring system comprising a combination of elements selected from aromatic rings, cycloalkane, heterocyclic rings, alkyl chains, and suitable C-, N-, O-, S-, and/or halogen-containing substituents, a hydrogen bond donor or a hydrogen bond acceptor, a sulfur-containing group (e.g., thiol, sulfide, disulfide, sulfoxide, sulfone), a group selected from CHR⁴SO₂R⁵ or NR⁴SO₂R⁵, in which R⁴ comprises or consists of: H, alkyl group (e.g., straight-chain alkyl (e.g., methane, ethane, propane, butane, pentane, hexane, etc.), branched alkyl group (e.g., iso-propane, 2-methyl-hexane, 3-methyl,2-propyl-octane, etc.), cycloalkyl (e.g., cyclopropane, cyclobutane, cyclopentane, cyclohexane, cyclooctane, etc.), branched cyclic alkyl (e.g., methylcyclohexane, ethylcyclobutane, propylcyclohexane, etc.)), a substituted alkyl group (e.g., halogen-substituted alkyl group (e.g., trihaloethane (e.g., trifluoroethane), alkylnitrile group (e.g. ethanenitryle group, CH₂CN), alkoxy group (e.g., ether, alcohol, etc.), alkylamine (e.g., primary amine (e.g., ethylamine, iso-butylamine, n-propylamine, sec-butylamine, iso-propylamine, iso-amylamine, methylamine, dimethylamine, n-amylamine, etc.), secondary amines (e.g., dimethylamine, methylethanolamine, diphenylamine, etc.), tertiary amine (e.g., trimethylamine, triphenylamine, etc.), a carbocyclic ring, a substituted cycloalkyl group (e.g., halogen-substituted cycloalkyl group, alkyl-substituted cycloalkyl group, cycloalkoxy group, cyclolkylamine, etc.) and R⁵ comprises or consists of: H, alkyl group (e.g., straight-chain alkyl (e.g., methane, ethane, propane, butane, pentane, hexane, etc.), branched alkyl group (e.g., iso-propane, 2-methyl-hexane, 3-methyl,2-propyl-octane, etc.), cycloalkyl (e.g., cyclopropane, cyclobutane, cyclopentane, cyclohexane, cyclooctane, etc.), branched cyclic alkyl (e.g., methylcyclohexane, ethylcyclobutane, propylcyclohexane, etc.)), a substituted alkyl group (e.g., halogen-substituted alkyl group (e.g., trihaloethane (e.g., trifluoroethane), halomethane (e.g., fluoromethane), dihalomethane (e.g., difluoromethane), trihalomethane (e.g., trifluoromethane), etc.), alkoxy group (e.g., ether, alcohol, etc.), alkylamine (e.g., primary amine (e.g., ethylamine, iso-butylamine, n-propylamine, sec-butylamine, iso-propylamine, iso-amylamine, methylamine, dimethylamine, n-amylamine, etc.), secondary amines (e.g., dimethylamine, methylethanolamine, diphenylamine, etc.), tertiary amine (e.g., trimethylamine, triphenylamine, etc.), thioalkyl, a substituted cycloalkyl group (e.g., halogen-substituted cycloalkyl group, cycloalkoxy group, cycloalkylamine, etc.), a ketone, a carbocyclic ring, an aromatic ring, a substituted aromatic ring (e.g., branched aromatic ring (e.g., ethylbenzene, methyl benzene, etc.), halobenzene (e.g., chlorobenzene, fluorobenzene, etc.)), a heterocyclic aromatic ring (e.g., comprising one or more nitrogen, oxygen and/or sulfur members which may be non-substituted or substituted with alkyl, aryl, halogen, hydrogen bond donor or acceptor), a heterocyclic non-aromatic ring (e.g., comprising carbon and one or more nitrogen, oxygen and/or sulfur members), carbocyclic or heterocyclic aromatic ring comprising carbon atoms and one or more nitrogen, oxygen and/or sulfur members fused to another aromatic ring, a multi-ring system comprising a combination of elements selected from aromatic rings, cycloalkane, heterocyclic rings, alkyl chains, and suitable C-, N-, O-, S-, and/or halogen-containing substituents, a hydrogen bond donor or a hydrogen bond acceptor, and/or combinations thereof, R⁵ might also be a part of the 3-8 member aromatic or non-aromatic ring comparising C, N, O, S (e.g. compounds 52,53,55). In some embodiments, Z comprises:

In some embodiments, Z is selected from: dimethyl sulfone, amino-sulfonyl-methane (NHSO₂CH₃), amino-sulfonyl-amine (NHSO₂NH₂), methyl-sulfonyl-amino (CH₃SO₂NH₂, methylamino-sulfonyl-methane (NCH₃SO₂CH₃; See e.g., compound 46), amino-sulfonyl-amino-methane (NHSO₂NHCH3), amino-sulfonyl-ethane-2-amine (NHSO₂CH₂CH₂NH₂), amino-sulfonyl-ethane (NHSO₂CH₂CH₃), amino-sulfonyl-dimethylamine (NHSO₂N(CH3)₂; See, e.g., compound 51), amino-sulfonyl-isopropane (NHSO₂ ¹Pr), amino-sulfonyl-heterocycloalkane (e.g., amino-sulfonyl-1-pyridine, amino-sulfonyl-1-oxazine, amino-sulfonyl-1-pyrazine, etc.), amino-sulfonyl-alkyl (e.g., amino-sulfonyl-methane (NHSO₂CH₃), amino-sulfonyl-ethane (NHSO₂CH₂CH₃), amino-sulfonyl-propane (NHSO₂(CH₂)₂CH₃), amino-sulfonyl-butane (NHSO2(CH₂)₃CH₃), etc.), sulfinic acid, thiocyanate, etc.), and/or combinations thereof.

In some embodiments, R1 of subscaffold 2 is selected from an alkyl (e.g., branched (e.g., isopropyl), straight chain (e.g., propyl), cycloalkyl (e.g., cyclopropyl)), heteroalkyl (e.g., methyl propyl ether), alkyl-substituted aryl (e.g., ethylbenzene), substituted alkyl (e.g., halo-substituted alkyl (e.g., trihalomethyl group (e.g., trifluoromethyl group), trihaloethyl group (e.g., trifluoroethyl group), trihalopropyl (e.g., trifluoropropyl), trihalobutyl group (e.g., trifluorobutyl group), trihaloisopropyl(e.g., trifluoroisopropyl), 1-fluoro,2-trifluoro, ethane, trifluoroethanol), alcohol, amino, etc. (See, e.g., Table 2).

In some embodiments, R2 of subscaffold 2 is selected from a halogen (e.g., Cl, F, Br, I), alkyl (e.g., branched, straight chain (e.g., methyl), cycloalkyl, heteroalkyl, etc.), alkyl-substituted aryl, substituted alkyl (e.g., halo-substituted alkyl, alcohol, amino, etc.), alcohol (e.g. OH, methanol, ethanol, etc), SH, NH₂, etc.

In some embodiments, R3 of subscaffold 2 is selected from hydrogen, alkyl (C₁-C₅), haloalkyl (e.g. CF₃), alcohol (e.g., OH, methanol, ethanol, isopropanol, etc.), alkoxy (e.g. methoxy, ethoxy, etc), amine (e.g. —NH2), halogen (Cl, Br, F, I), methyl-sulfonyl-amine (CH₂SO₂NH₂), etc. (See, e.g., Table 2). In some embodiments, R3 can be present at more than 1 position of the phenyl ring.

In some embodiments, R3 of subscaffold 2 is present at the ortho or meta positions of the benzene ring. In some embodiments, R3 groups are present at two or more positions on the benzene.

In some embodiments, Z of subscaffold 2 comprises an H, alkyl group, amino group (e.g., primary, secondary, alkylamine, aminoalkyl, etc.), halogen, heterocycle, sulfone-containing group (see e.g., Table 2), CHR⁴SO₂R⁵ or NR⁴SO₂R⁵ in which R4 and R5 are independently selected from an alkyl (e.g., branched, straight chain (e.g., methyl), cycloalkyl, heteroalkyl, etc.), substituted or non-substituted heterocycle comprising one or more N, C, O or S, thrihaloalkane, amino, alcohol, alkyl-substituted aryl, substituted or non-substituted heterocyclic ring, substituted alkyl (e.g., halo-substituted alkyl, alcohol, amino, cyano, aryl, heterocyclic ring, etc.), cyano, etc.

In some embodiments, R3 and Z groups (e.g., (CH)₂NH in compound 81) bridge two positions of the benzene ring of subscaffold 2.

In some embodiments, L of subscaffold 2 is alkylene (e.g. ethylene, —CH₂—CH₂—, etc) or oxalkylene (e.g. —O—, —CH₂—O—CH₂) groups.

In some embodiments, Q of subscaffold 2 is alkylene (e.g. Cl-05) or oxyalkylene (e.g. —CH₂—O—CH₂—).

In some embodiments, compositions comprising one or more of compound 43-104 and 284-287 of Table 2 are provided.

In some embodiments, the thienopyrimidine class compound is of a general formula of:

wherein R1, R2, R3, and R4 independently comprise or consist of: H, alkyl group (e.g., straight-chain alkyl (e.g., methane, ethane, propane, butane, pentane, hexane, etc.), branched alkyl group (e.g., iso-propane, 2-methyl-hexane, 3-methyl,2-propyl-octane, etc.), cycloalkyl (e.g., cyclopropane, cyclobutane, cyclopentane, cyclohexane, cyclooctane, etc.), branched cyclic alkyl (e.g., methylcyclohexane, ethylcyclobutane, propylcyclohexane, etc.)), a substituted alkyl group (e.g., halogen-substituted alkyl group (e.g., mono-, di-, tetra-,penta- and trihaloethane (e.g., trifluoroethane), halomethane (e.g., fluoromethane), dihalomethane (e.g., difluoromethane), trihalomethane (e.g., trifluoromethane), etc.), alkoxy group (e.g., ether, alcohol, etc.), alkylamine (e.g., primary amine (e.g., ethylamine, iso-butylamine, n-propylamine, sec-butylamine, iso-propylamine, iso-amylamine, methylamine, dimethylamine, n-amylamine, etc.), secondary amines (e.g., dimethylamine, methylethanolamine, diphenylamine, etc.), tertiary amine (e.g., trimethylamine, triphenylamine, etc.), thioalkyl, combinations thereof, etc.), a substituted cycloalkyl group (e.g., halogen-substituted cycloalkyl group, cycloalkoxy group, cycloalkylamine, etc.), a halogen (e.g., F, Cl, Br, I, and At), a ketone, a carbocyclic ring, an aromatic ring, a substituted aromatic ring (e.g., branched aromatic ring (e.g., ethylbenzene, methyl benzene, etc.), halobenzene (e.g., chlorobenzene, fluorobenzene, etc.)), a heterocyclic aromatic ring (e.g., comprising one or more nitrogen, oxygen and/or sulfur members which may be non-substituted or substituted with alkyl, aryl, halogen, hydrogen bond donor or acceptor), a heterocyclic non-aromatic ring (e.g., comprising carbon and one or more nitrogen, oxygen and/or sulfur members), carbocyclic or heterocyclic aromatic ring comprising carbon atoms and one or more nitrogen, oxygen and/or sulfur members fused to another aromatic ring, a multi-ring system comprising a combination of elements selected from aromatic rings, cycloalkane, heterocyclic rings, alkyl chains, and suitable C-, N-, O-, S-, and/or halogen-containing substituents, or a hydrogen bond donor or a hydrogen bond acceptor, and/or combinations thereof; wherein R5 comprises or consists of: H, alkyl group (e.g., straight-chain alkyl (e.g., methane, ethane, propane, butane, pentane, hexane, etc.), branched alkyl group (e.g., iso-propanol, 2-methyl-hexane, 3-methyl,2-propyl-octane, etc.), cycloalkyl (e.g., cyclopropane, cyclobutane, cyclopentane, cyclohexane, cyclooctane, etc.), branched cyclic alkyl (e.g., methylcyclohexane, ethylcyclobutane, propylcyclohexane, etc.)), a substituted alkyl group (e.g., halogen-substituted alkyl group (e.g., trihaloethane (e.g., trifluoroethane), halomethane (e.g., fluoromethane), dihalomethane (e.g., difluoromethane), trihalomethane (e.g., trifluoromethane), etc.), alkoxy group (e.g., ether, alcohol, etc.), alkylamine (e.g., primary amine (e.g., ethylamine, iso-butylamine, n-propylamine, sec-butylamine, iso-propylamine, iso-amylamine, methylamine, dimethylamine, n-amylamine, etc.), secondary amines (e.g., dimethylamine, methylethanolamine, diphenylamine, etc.), tertiary amine (e.g., trimethylamine, triphenylamine, etc.), thioalkyl, combinations thereof, etc.), amide, alkylamide, a substituted cycloalkyl group (e.g., halogen-substituted cycloalkyl group, cycloalkoxy group, cycloalkylamine, etc.), a halogen (e.g., F, Cl, Br, I, and At), a ketone, a carbocyclic ring, an aromatic ring, a substituted aromatic ring (e.g., branched aromatic ring (e.g., ethylbenzene, methyl benzene, etc.), halobenzene (e.g., chlorobenzene, fluorobenzene, etc.)), a heterocyclic aromatic ring (e.g., comprising one or more nitrogen, oxygen and/or sulfur members which may be non-substituted or substituted with alkyl, aryl, halogen, hydrogen bond donor or acceptor), a heterocyclic non-aromatic ring (e.g., comprising carbon and one or more nitrogen, oxygen and/or sulfur members), carbocyclic or heterocyclic aromatic ring comprising carbon atoms and one or more nitrogen, oxygen and/or sulfur members fused to another aromatic ring, a multi-ring system comprising a combination of elements selected from aromatic rings, cycloalkane, heterocyclic rings, alkyl chains, and suitable C-, N-, O-, S-, and/or halogen-containing substituents, or a hydrogen bond donor or a hydrogen bond acceptor, and/or combinations thereof. In some embodiments, R5 is present at the ortho, meta, or para position of the benzene ring of subscaffold 3. In some embodiments, the benzene ring of subscaffold 3 comprises R5 groups at two or more (e.g., 2, 3, 4, or 5) positions. In some embodiments, an R5 group bridges two positions of the benzene ring of subscaffold 3 (See e.g., 3-keto,4-amino-propane of compound 136 of Table 3); and wherein Y is N or C, and wherein when Y is C the Y position may be substituted with R^(a), with R^(a) consisting of or comprising an alkyl (e.g., branched (e.g., isopropyl), straight chain (e.g., propyl), cycloalkyl (e.g., cyclopropyl)), heteroalkyl (e.g., methyl propyl ether), alkyl-substituted aryl (e.g., ethylbenzene), substituted alkyl (e.g., halo-substituted alkyl (e.g., trihalomethyl group (e.g., trifluoromethyl group), monohaloalkyl group (e.g. monofluoroethyl group), dihaloalkyl group (e.g. difluoroethyl group), trihaloethyl group (e.g., trifluoroethyl group), trihalopropyl (e.g., trifluoropropyl ((CH₂)₂CF₃), trihalobutyl group (e.g., trifluorobutyl group ((CH₂)₃CF₃)), trihaloisopropyl (e.g., trifluoroisopropyl, 1-fluoro,2-trifluoro, ethane, 1-trifluoro,2-ethanol, alcohol (e.g., (CH₂)_(n)OH, wherein n=0-10), alkoxy (e.g., (CH₂)_(n)—OR, wherein n=0-10, wherein R is alkyl, (CH₂)_(n)-aryl, (CH₂)_(n)-aromatic, (CH₂)_(n)-heterocycle, substituted or non-substituted aryl, aromatic or non-aromatic heterocycle with one or more N, S, O, etc.), amino (e.g., alkyl amine, amino alkyl, etc.), cyano, sulfonyl, methoxy, aldehyde, heterocycle, aromatic, combinations thereof, etc.; and wherein L is present or absent and comprises alkylene (e.g. methylene, —CH₂—, ethylene, —CH₂—CH₂—, propylene, —CH₂—CH₂—CH₂—, etc) or oxalkylene (e.g. —O—, —CH₂—O—CH₂) groups.

In some embodiments, R1 of subscaffold 3 comprises or consists of trifluoroethane. In some embodiments, R1 of subscaffold 3 comprises or consists of trihaloethane (e.g., trifluoroethane), 2-dihalo-4-butanol (e.g., 2-difluoro-4-butanol, etc.), an alkyl chain (e.g., straight chain alkyl (e.g., methane, ethane, propane, butane, etc.), branched alkyl, cycloalkyl, or combinations thereof), 2-dihalo-propane (e.g., 2-difluoro-propane, etc.), etc. (See Table 3).

In some embodiments, R2 of subscaffold 3 is selected from a halogen (e.g., Cl, F, Br, I), alkyl (e.g., branched, straight chain (e.g., methyl), cycloalkyl, heteroalkyl, etc.), alkyl-substituted aryl, substituted alkyl (e.g., halo-substituted alkyl, alcohol, amino, etc.), alcohol (—OH, —CH₂OH, etc) SH, NH₂, etc.

In some embodiments, R3 of subscaffold 3 consists of H. In some embodiments, R3 of subscaffold 3 comprises or consists of an alkyl (e.g., methane, ethane, propane, butane, etc.), amine (e.g., NH₂, NH-alkyl (e.g., NH-methyl, NH-ethyl, NH—CH₂-Ph, etc.), NH-alcohol (e.g., NH—CH₂—CH₂—OH), etc.), alcohol (e.g., methanol, ethanol, butanol, propanol, —CH₂—CHOHCH₂OH, etc.), halo-substituted alkyl, combinations thereof, etc. (See Table 3). In some embodiments, R3 is fused in a ring with R2 (See, e.g. compound 158).

In some embodiments, R4 of subscaffold 3 comprises or consists of an amine (e.g., NH₂, alkylamine (e.g., methylamine, ethylamine, propylamine, etc.), aminoalkyl (e.g., straight chain alkyl, cycloalkyl, or combinations thereof (See, e.g., compound 171)), amino-alkyl-phenyl (e.g., amino-methyl-phenyl, amino-ethyl-phenyl, etc.), etc.), alcohol (e.g., OH, methanol, ethanol, propanol, isopropanol, etc.), substituted amine (—NHR³) or substituted alcohol (—OR³), in which R³ is alkyl, alkyl-aryl (substituted and non-substituted), alkyl-cycloalkyl (substituted and non-substituted), alkyl-aromatic ring substituted or non-substituted, alkyl-non aromatic ring (C, N, O, S) substituted or non-substituted, or any of the R4 groups depicted in Tables 4, 5, or 7. In some embodiments, R4 comprises or consists of aminomethyl phenyl (See, e.g. compound 167), aminoethyl phenyl (See, e.g., compound 168), amino-methyl-cyclopentane (See, e.g., compound 169), aminomethyl, n-methanal pyrrolidine, aminoethyl cyclopentane, aminomethyl (NHCH₃), methylamine (CH₂NH₂), n-sulfonyl-methyl pyrrolidine (See, e.g., compound 173), O-methyl phenyl (See, e.g. compound 174), etc., see Table 4.

In some embodiments, R5 of subscaffold 3 comprises or consists of: H, an alcohol (e.g., OH, methanol, ethanol, etc.), alkane, cycloalkane (e.g., substituted cycloalkane (e.g., cyanocyclopropane)), amine, halogen (e.g., chlorine, fluorine, bromine, iodine, etc.), heterocyclic ring (e.g., attached at any position on the heterocyclic ring: morpholine, piperidine, methylpiperidine, pyrrole, thiophene, piperazine, etc.), alkylamine (e.g., methylamine, ethylamine, propylamine, 1,4-dimethyl-piperazine, etc.), alkylalkohol (e.g. —CH₂OH), alkoxy, carboxamido, O-dihalomethane, sulfonyl-amine, trihalomethane (e.g., trifluoromethane), etc. In some embodiments, the benzene ring of subscaffold 3 comprises R5 groups at two or more (e.g., 2, 3, 4, or 5) positions.

In some embodiments, L of subscaffold 3 is alkylene (e.g. ethylene, —CH₂—CH₂—, compound 135) or oxalkylene (e.g. —O—, —CH₂—O—CH₂) groups.

In some embodiments, compositions comprising one or more of compound 105-159 of Table 3, 165-174 of Table 4 and 280 and 282 of Table 7 are provided.

In some embodiments, the thienopyrimidine class compound is of a general formula of:

wherein R1, R2, R3, R4, R5, R6, R7, R8 each independently comprise or consist of: H, alkyl group (e.g., straight-chain alkyl (e.g., methane, ethane, propane, butane, pentane, hexane, etc.), branched alkyl group (e.g., iso-propyl, 2-methyl-hexane, 3-methyl,2-propyl-octane, etc.), cycloalkyl (e.g., cyclopropane, cyclobutane, cyclopentane, cyclohexane, cyclooctane, etc.), branched cyclic alkyl (e.g., methylcyclohexane, ethylcyclobutane, propylcyclohexane, etc.)), a substituted alkyl group (e.g., halogen-substituted alkyl group (e.g., trihaloethane (e.g., trifluoroethane), halomethane (e.g., fluoromethane), dihalomethane (e.g., difluoromethane), trihalomethane (e.g., trifluoromethane), etc.), alkoxy group (e.g., ether, alcohol, etc.), amine, alkylamine (e.g., primary amine (e.g., ethylamine, iso-butylamine, n-propylamine, sec-butylamine, iso-propylamine, iso-amylamine, methylamine, dimethylamine, n-amylamine, etc.), secondary amines (e.g., dimethylamine, methylethanolamine, diphenylamine, etc.), tertiary amine (e.g., trimethylamine, triphenylamine, etc.), thioalkyl, combinations thereof, etc.), a substituted cycloalkyl group (e.g., halogen-substituted cycloalkyl group, cycloalkoxy group, cycloalkylamine, etc.), a halogen (e.g., F, Cl, Br, I, and At), a ketone, an amide, an alkylamide, a cyano group, methyl carbonitrile (e.g. CH₂CN), —SO₂CH₃ group, sulfonyl group, a carbocyclic ring, an aromatic ring, a substituted aromatic ring (e.g., branched aromatic ring (e.g., ethylbenzene, methyl benzene, etc.), halobenzene (e.g., chlorobenzene, fluorobenzene, etc.)), a heterocyclic aromatic ring (e.g., comprising one or more nitrogen, oxygen and/or sulfur members which may be non-substituted or substituted with alkyl, aryl, halogen, hydrogen bond donor or acceptor), a substituted or non-substituted heterocyclic non-aromatic ring (e.g., comprising carbon and one or more nitrogen, oxygen and/or sulfur members), carbocyclic or heterocyclic aromatic ring comprising carbon atoms and one or more nitrogen, oxygen and/or sulfur members fused to another aromatic ring, a multi-ring system comprising a combination of elements selected from aromatic rings, cycloalkane, heterocyclic rings, alkyl chains, and suitable C-, N-, O-, S-, and/or halogen-containing substituents, or a hydrogen bond donor or a hydrogen bond acceptor, and/or combinations thereof; and

wherein any of the H atoms, R6, R7 and R8 on the indole of subscaffold 4 may be replaced with one of: halogen (e.g., F, Cl, Br, I, etc.), alcohol (e.g., OH, methanol, ethanol, etc.), alkyl (C1-C5), alkoxy (e.g. methoxy, ethoxy, etc), amine (e.g. NH₂, methylamine, ethylamine, etc), cyano group (e.g., CN, methyl carbonitrile, ethyl carbonitrile, etc.), an amide (e.g. CONH₂, acetamide, etc), —SO₂CH₃ group; wherein R6 can be present on either the phenyl and/or pyrrole portion of the indole ring, and wherein R6 can be present at one or more of the positions of the phenyl and/or pyrrole portion of the indole ring that are not otherwise occupied by a substituent; and wherein Y is N or C, and wherein when Y is C the Y position may be substituted with R^(a), with R^(a) consisting of or comprising an alkyl (e.g., branched (e.g., isopropyl), straight chain (e.g., propyl), cycloalkyl (e.g., cyclopropyl)), heteroalkyl (e.g., methyl propyl ether), alkyl-substituted aryl (e.g., ethylbenzene), substituted alkyl (e.g., halo-substituted alkyl (e.g., trihalomethyl group (e.g., trifluoromethyl group), monohaloalkyl group (e.g. monofluoroethyl group), dihaloalkyl group (e.g. difluoroethyl group), trihaloethyl group (e.g., trifluoroethyl group), trihalopropyl (e.g., trifluoropropyl ((CH₂)₂CF₃), trihalobutyl group (e.g., trifluorobutyl group ((CH₂)₃CF₃)), trihaloisopropyl (e.g., trifluoroisopropyl, 1-fluoro,2-trifluoro, ethane, 1-trifluoro,2-ethanol), alcohol (e.g., (CH₂)_(n)OH, wherein n=0-10), alkoxy (e.g., (CH₂)_(n)—OR, wherein n=0-10, wherein R is alkyl, (CH₂)_(n)-aryl, (CH₂)_(n)-aromatic, (CH₂)_(n)-heterocycle, substituted or non-substituted aryl, aromatic or non-aromatic heterocycle with one or more N, S, O, etc.), amino (e.g., alkyl amine, amino alkyl, etc.), cyano, sulfonyl, methoxy, aldehyde, heterocycle, aromatic, combinations thereof, etc.;

wherein L is present or absent, and if present it comprises alkylene (e.g. methylene, —CH₂—, ethylene, —CH₂—CH₂—, propylene, —CH₂—CH₂—CH₂—, etc) or oxalkylene (e.g. —O—, —CH₂—O—CH₂) groups.

In some embodiments, R1 of subscaffold 4 comprises or consists of monohaloethane, dihaloethane or trihaloethane (e.g., monofluorothane, difluoroethane and trifluoroethane) group, (see Table 5).

In some embodiments R2 is H or another R2 substituent described herein.

In some embodiments R3 of subscaffold 4 comprises or consists of an alkyl (e.g., methane, ethane, propane, butane, etc.), amine (e.g., NH₂, NH-alkyl (e.g., NH-methyl, NH-ethyl, NH—CH₂-Ph, etc.), NH-alcohol (e.g., NH—CH₂—CH₂—OH), etc.), an alcohol (e.g., methanol, ethanol, butanol, propanol, CH₂CHOHCH₂OH, etc.), a heterocyclic ring, an alkyl-heterocyclic ring (e.g., ethyl-morpholine (see compound 238), propyl-indole, etc.), etc. In some embodiments, R3 is fused in a ring with R2 (See, e.g. compound 158).

In some embodiments R4 comprises or consists of amine (e.g. —NH₂), NH—(CH₂)₁₋₆-phenyl (see compound 288), NH—(CH₂)₁₋₆-(substituted aromatic ring) (see compound 289), aminomethyl, aminoakyl N-formylpyrrolidine (see compound 161 in Table 5), aminoakyl N-sulfonylpyrrolidine (see compound 173 in Table 5), —CH₂—OH (see compounds 163-164 in Table 5).

In some embodiments, R5 is —CH₂—OH (see compound 211, Table 5).

In some embodiments, R6 is an alkyl (e.g., methane, ethane, propane, butane, etc.), cycloalkane (e.g., cyclopropane (See, e.g., compound 293), cyclobutane, cyclopentane, cyclohexane, etc.), halogen (e.g., Br, F, Cl, I, etc.), haloalkane (e.g., monohaloalkane, dihaloalkane (e.g., difluoromethane (See, e.g., compound 305)), trihaloalkane (e.g., trichloroethane)), amine (e.g., NH₂, NH-alkyl (e.g., NH-methyl, NH-ethyl, NH—CH₂-Ph, etc.) alkyl-amine (e.g., (CH₂)₁₋₆—NH₂)), O-alkyl (e.g., OCH₃, OCH₂CH₃, etc.), NH-alcohol (e.g., NH—CH₂—CH₂—OH), etc.), an alcohol (e.g., methanol, ethanol, butanol, propanol, CH₂CHOHCH₂OH, etc.), or any R6 group of Tables 4, 5, or 7. In some embodiments, R6 is present on either the phenyl and/or pyrrole portions of the indole ring. In some embodiments R6 on indole ring is present at more than one position on the phenyl and/or pyrrole portions of the indole ring.

In some embodiments, R7 is H, alkyl (e.g., methyl, ethyl, propyl, butyl, etc.), haloalkane, cycloalkyl (e.g., cyclopropane (e.g., methyl cyclopropane), cyclobutane, cyclopentane, cyclohexane, etc.), an alcohol (e.g., OH, methanol, ethanol, propanol, butanol, etc.), a substituted or non-substituted heterocycle (See, e.g., compound s 427 and 430), a substituted or non-substituted heteroaromatic ring (e.g., pyrazole, triazole (e.g., 1,2,4 triazole), isoxazole (e.g., dimethyl isoxazole), (CH₂)_(n)—OR (wherein n=1-10 and R is an aromatic ring, heteroaromatic ring, cycloalkyl, heterocycle, substituted ring, etc.), alkyl-heterocycle (e.g., (CH₂)₁₋₆-piperidine (See, e.g., compound 328), (CH₂)₁₋₆-piperazine (See, e.g., compound 336), (CH₂)₁₋₆-pyrazole (See, e.g., compounds 309, 324, 388)), (CH₂)_(n)—R (wherein n=1-10 and R is an aromatic ring, heteroaromatic ring, cycloalkyl, heterocycle, substituted ring, etc.), (CH₂)_(n)—O—(CH₂)_(m)—R (wherein n=1-10, m=1-10, and R is an aromatic ring, heteroaromatic ring, cycloalkyl, heterocycle, substituted ring, etc.), substituted or non-substituted alkyl-heteroaromatic ring (e.g. CH₂-thiadiazole (See, e.g., compound 322), CH₂-thiadiazole —CH₃, CH₂-thiazolidine (See, e.g., compound 323), CH₂-pyridine (See, e.g., compound 329), CH₂-pyrazole (See, e.g., compound 309), CH₂-triazole (See, e.g., compound 311), CH₂-oxazole (See, e.g., compounds 353, 361), CH₂—CH₂-triazole, ethyl-thiomorpholine (See, e.g., compound 360), etc), amide (e.g. acetamide, see, e,g, compound 189), alkyl-SO₂-alkyl (See, e.g., compounds 354, 395), amine (e.g., NH₂, NH-alkyl (e.g., NH-methyl, NH-ethyl, NH—CH₂-Ph, etc., NH-alcohol (e.g., NH—CH₂—CH₂—OH), etc.), (CH₂)₁₋₆CONH₂ (See, e.g., compound 310), substituted or non-substituted alcohol (e.g., methanol, ethanol, butanol, propanol, CH₂CHOHCH₂OH, etc.), (CH₂)₁₋₆—CO-halogen (See, e.g., compound 306), (CH₂)₁₋₆—CO—NH₂ (See, e.g., compound 307), alkyl-diol (See, e.g., compounds 308, 338, 346, 348), diol-substituted alkyl or heteroalkyl chain with a terminal substitution (wherein the terminal substitution is selected from amide, cycloalkyl, heterocycle, aromatic ring, heteroaromatic ring, any of which may be further substituted (See, e.g., compounds 333, 338, 346, 348, 413 and 427-430)), or any R7 substituents in the compounds of Tables 4, 5, or 7 (See, e.g., compounds 312-320, 330, 331, 333, 334, 337, 339-345, 350-351, 355-359, 362-365, 367-379, 394, 396-406).

In some embodiments, R8 of subscaffold 4 comprises or consists of: H, alkyl (e.g., methyl, ethyl, propyl, butyl, etc.), cycloalkyl (e.g., cyclopropane (e.g., methyl cyclopropane), cyclobutane, cyclopentane, cyclohexane, etc.), a primary alcohol (e.g., OH, methanol, ethanol, propanol, butanol, etc.), a secondary alcohol, a substituted or non-substituted heteroaromatic ring (e.g., pyrazole, triazole (e.g., 1,2,4 triazole, 1,2,3 triazole (e.g., alkyl-substituted triazole (See, e.g., compound 303))), isoxazole, isopropylisopropanolamine (CH₂CHOHCH₂NHCH(CH₃)₂); sulfonamide, a cyano group (e.g., CN, methyl carbonitrile, ethyl carbonitrile, propyl carbonitrile, etc.), amide (e.g., CONH₂, methylcarboxamido (e.g., CH₂CONH₂, CH₂CONH—C₁₋₆ (See compound 291)), ethyl carboxamido (CH₂CH₂CONH₂), carboxyamido-methane (e.g., CONHCH₃ or NHCOCH₃), etc.), CH₂CHOHCH₂OH (See, e.g., compound 300), methylsulfonyl, sulfonamide, ketone (e.g., ═O), or any R8 substituents in the compounds of Tables 4, 5, or 7 (See e.g., compounds 292, 297, etc.).

In some embodiments, the substituted indole ring of subscaffold 4 is: cyano substituted (e.g., 1-carbonitrile, 2-carbonitrile, etc.), methyl-carbonitrile substituted (e.g., 5-methyl-carbonitrile, etc.), methylcyclopropane substituted (e.g., 1-methylcyclopropane), halo-substituted (e.g., 3-halo (e.g., 3-fluoro, 4-fluoro, 6-fluoro, etc.)), alkyl substituted (e.g., 1-alkyl (e.g., 1-methyl, 1-ethyl, 1-propyl, etc.)), alcohol-substituted (e.g., OH substituted (e.g., 6-OH), methanol substituted (e.g., 1-methanol), ethanol substituted (e.g., 1-ethanol), etc.), O-methyl substituted (e.g., 4-O-methyl, 6-O-methyl, etc.), alkoxy substituted (e.g. 1-O-methoxy, 1-O-ethoxy, etc), heterocyclic aromatic ring (or ring system) substituted (e.g., imidazole), amine substituted (e.g., NH₂, methylamine, ethylamine (e.g., 1-ethylamine, etc.), aminomethyl, etc.), dihydroxy substituted (e.g., 1,2-propanediol, etc.), amide substituted (e.g., 1-propanamide), acetamide, 1-methyl 1,2,3-triazole substituted, 1-ethyl imidazole substituted, heterocycle substituted, carboxamido substituted (e.g., 1-carboxamido), sulfonyl substituted (e.g., 1-sulfonyl methyl (SO₂CH₃), ether substituted (e.g., isopropanol methyl ether (CH₂CHOHCH₂CH₃), keto-substituted (e.g., 1-keto), isopropanol-amine-isopropyl substituted (CH₂CHOHCH₂NHCH(CH₃)₂, combinations thereof depicted in Table 4, or combinations thereof not depicted in Table 4).

In some embodiments, L is absent.

In some embodiments, compositions comprising one or more of compound 160-164, 290-417, 423-430 (Table 4) and 175-252 of Table 5 and compounds 278, 279, 281 of Table 7 are provided.

In some embodiments, the thienopyrimidine class compound is of a general formula of:

wherein R1, R2, R3, R4, R5, R6, R7, R8, L, Y, and any substituents thereof each independently comprise or consist of any of the groups and substituents provided above for subscaffold 4; and wherein E and G are independently N or C, wherein E and G are independently and optionally substituted with a R6.

In some embodiments, compositions comprising one or more of compound 380 and/or 422, are provided. In some embodiments, subscaffold 4b is modified with any of the substituents described or depicted for subscaffold 4.

In some embodiments, the thienopyrimidine class compound is of a general formula of:

wherein R1, R2, R3, R4, R5, R6, R7, R8, L, Y, and any substituents thereof each independently comprise or consist of any of the groups and substituents provided above for subscaffold 4; wherein X is (CH₂)₀₋₆; and wherein J and M are independently N, O, S, or C; wherein R9 comprises or consists of: H, alkyl (e.g., methyl, ethyl, propyl, isopropyl, etc.), CO-alkyl (formyl, acetyl, propanoyl, etc.), CO-alkenyl (e.g., CO-ethenyl, CO-propenyl), CO-alkynyl (e.g., CO-ethynyl, CO-propynyl), CO—(CH₂)₁₋₆-aryl, CO—(CH₂)₁₋₆-heteroaryl, CO—(CH₂)₁₋₃-trifluoromethane, CO—(CH₂)₁₋₆-cycloalkane, alcohol (e.g., OH, methanol, ethanol, propanol, etc.), CONH₂, CO(CH₂)₁₋₆, O₂ (See, e.g., compound 368), SO₂NH₂, SO₂-amino-dialkyl (See, e.g., compound 375), SO₂—NH-alkyl (See, e.g., compound 405), CO-amino-dialkyl (See, e.g., compound 376), SO₂—(CH₂)₁₋₆ (See, e.g., compound 377), SO₂— alkenyl (e.g., SO₂-ethenyl, SO₂-propenyl), SO₂-alkynyl (e.g., SO₂-ethynyl, SO₂-propynyl), CO—(CH₂)₁₋₆, or other suitable substituents described herein; and wherein R10 comprises or consists of: H, alkyl (e.g., methyl, ethyl, propyl, etc.), ═O, trifluoromethane, alcohol (e.g., OH, methanol, ethanol, propanol, etc.), or other suitable substituents described herein.

In some embodiments, compositions comprising one or more of compounds: 336, 337, 339-344, 355-358, 360, 364, 366-370, 372, 375-378, 393, 394, 396-406, 426 and/or 428-429 are provided. In some embodiments, subscaffold 4c is modified with any of the substituents described or depicted for subscaffold 4.

In some embodiments, the thienopyrimidine class compound is of a general formula of:

wherein R1, R2, R3, R4, R5, R6, R7, R8, L, Y, and any substituents thereof each independently comprise or consist of any of the groups and substituents provided above for subscaffold 4; wherein T is a heteroaromatic ring or cycloalkane; and wherein R11 comprises or consists of: H, alkyl (e.g., methyl, ethyl, propyl, isopropyl, etc.), alcohol (e.g., OH, methanol, ethanol, propanol, etc.), O-alkyl, O—(CH₂)₁₋₃-cycloalkane (See, e.g., compound 312), (CH₂)₁₋₃—O—(CH₂)₁₋₃—O-alkyl (See, e.g., compound 313), (CH₂)₁₋₃—O—(CH₂)₁₋₃-cycloalkane (See, e.g., compound 318), (CH2)1-3-heteroaromatic (See, e.g., compounds 345 or 347), or any other suitable substituents described herein.

In some embodiments, T is a: 5-membered ring comprising carbon atoms and one or more of N, S, and/or O (e.g., pyrrole, furan, thiophene imidazole, pyrazole, oxazole, isoxazole, thizole, isothiazole, triazoles, furazan, oxadiazole, thiadiazole, dithiazole, tetrazole, etc.); 6-membered ring comprising carbon atoms and one or more of N, S, and/or O (e.g., pyridine, pyran, thiopyran, diazines, oxazine, thiazine, dioxine, dithiine, triazine, tetrazine, etc.); or a cyclopropane, cyclobutane, cyclopentane, or cyclohexane; and wherein R11 extends from any suitable position on the T ring.

In some embodiments, compositions comprising one or more of compounds: 303, 304, 312, 313, 318, 322, 323, 327, 331, 332, 334, 335, 345, 347, 349-353, 361, 365, 379, 381, 382, and 388-392 are provided. In some embodiments, subscaffold 4d is modified with any of the substituents described or depicted for subscaffold 4. In some embodiments, the thienopyrimidine class compound is of a general formula of:

wherein R1, R2, R3 and R4 independently comprise or consist of: H, alkyl group (e.g., straight-chain alkyl (e.g., methane, ethane, propane, butane, pentane, hexane, etc.), branched alkyl group (e.g., iso-propane, 2-methyl-hexane, 3-methyl,2-propyl-octane, etc.), cycloalkyl (e.g., cyclopropane, cyclobutane, cyclopentane, cyclohexane, cyclooctane, etc.), branched cyclic alkyl (e.g., methylcyclohexane, ethylcyclobutane, propylcyclohexane, etc.)), a substituted alkyl group (e.g., halogen-substituted alkyl group (e.g., trihaloethane (e.g., trifluoroethane), halomethane (e.g., fluoromethane), dihalomethane (e.g., difluoromethane), trihalomethane (e.g., trifluoromethane), etc.), alkoxy group (e.g., ether, alcohol, etc.), alkylamine (e.g., primary amine (e.g., ethylamine, iso-butylamine, n-propylamine, sec-butylamine, iso-propylamine, iso-amylamine, methylamine, dimethylamine, n-amylamine, etc.), secondary amines (e.g., dimethylamine, methylethanolamine, diphenylamine, etc.), tertiary amine (e.g., trimethylamine, triphenylamine, etc.), thioalkyl, combinations thereof, etc.), a substituted cycloalkyl group (e.g., halogen-substituted cycloalkyl group, cycloalkoxy group, cycloalkylamine, etc.), a halogen (e.g., F, Cl, Br, I, and At), a ketone, a carbocyclic ring, an aromatic ring, a substituted aromatic ring (e.g., branched aromatic ring (e.g., ethylbenzene, methyl benzene, etc.), halobenzene (e.g., chlorobenzene, fluorobenzene, etc.)), a heterocyclic aromatic ring (e.g., comprising one or more nitrogen, oxygen and/or sulfur members which may be non-substituted or substituted with alkyl, aryl, halogen, hydrogen bond donor or acceptor), a heterocyclic non-aromatic ring (e.g., comprising carbon and one or more nitrogen, oxygen and/or sulfur members), carbocyclic or heterocyclic aromatic ring comprising carbon atoms and one or more nitrogen, oxygen and/or sulfur members fused to another aromatic ring, a multi-ring system comprising a combination of elements selected from aromatic rings, cycloalkane, heterocyclic rings, alkyl chains, and suitable C-, N-, O-, S-, and/or halogen-containing substituents, or a hydrogen bond donor or a hydrogen bond acceptor, and/or combinations thereof; and

wherein any of the H atoms on the benzene ring of subscaffold 5 may be replaced with one of: halogen (e.g., F, Cl, Br, I, etc.), alcohol (e.g., OH, methanol, ethanol, etc.), cyano group (e.g., CN, methyl carbonitrile, ethyl carbonitrile, etc.), amine (e.g. NH₂, methylamine, ethylamine, etc.), trifluoromethane, alkyl (e.g., methane, ethane, propane, etc.), alkoxy (e.g. methoxy, ethoxy, etc), halogen substituted alkoxy (e.g. trifluoromethoxy), ketone, sulfonyl group (e.g. slufonamide), substituted or non-substituted heterocyclic ring (e.g. comprising carbon and one or more nitrogen oxygen and/or sulfur members), etc.; and wherein Y is N or C, and wherein when Y is C the Y position may be substituted with R^(a), with R^(a) consisting of or comprising an alkyl (e.g., branched (e.g., isopropyl), straight chain (e.g., propyl), cycloalkyl (e.g., cyclopropyl)), heteroalkyl (e.g., methyl propyl ether), alkyl-substituted aryl (e.g., ethylbenzene), substituted alkyl (e.g., halo-substituted alkyl (e.g., trihalomethyl group (e.g., trifluoromethyl group), monohaloalkyl group (e.g. monofluoroethyl group), dihaloalkyl group (e.g. difluoroethyl group), trihaloethyl group (e.g., trifluoroethyl group), trihalopropyl (e.g., trifluoropropyl ((CH₂)₂CF₃), trihalobutyl group (e.g., trifluorobutyl group ((CH₂)₃CF₃)), trihaloisopropyl (e.g., trifluoroisopropyl, 1-fluoro,2-trifluoro, ethane, 1-trifluoro,2-ethanol), alcohol (e.g., (CH₂)—OH, wherein n=0-10), alkoxy (e.g., (CH₂)_(n)—OR, wherein n=0-10, wherein R is alkyl, (CH₂)_(n)-aryl, (CH₂)_(n)-aromatic, (CH₂)_(n)-heterocycle, substituted or non-substituted aryl, aromatic or non-aromatic heterocycle with one or more N, S, O, etc.), amino (e.g., alkyl amine, amino alkyl, etc.), cyano, sulfonyl, methoxy, aldehyde, heterocycle, aromatic, combinations thereof, etc.;

In some embodiments, R1 of subscaffold 5 comprises or consists of: H, trifluoroethane, or another R1 group provided herein.

In some embodiments, R2 of subscaffold 5 comprises or consists of H.

In some embodiments, R3 of subscaffold 5 comprises or consists of alkyl group (e.g. n-buthyl, compound 264).

In some embodiments, R4 of subscaffold 5 comprises or consists of: H, aminosulfonyl, halogen (e.g., Cl, Br, F, I, etc.), a substituted or non-substituted heterocycle (e.g., piperidine, 1,4-oxazinane, piperazine, morpholine), cyano group (e.g., CN, cyanomethane, cyanoethane, etc.), alkoxy (e.g. O-methyl), amine (e.g. NH₂, methylamine, ethylamine, etc.), alcohol (e.g., OH, methanol, ethanol, etc.), trifluoromethane, ketone (e.g. acetyl), halogen substituted alkoxy (e.g. O-trifluoromethane, OCF₃, alkyl (e.g., methane, ethane, propane, etc.), etc.

In some embodiments, compositions comprising one or more of compound 253-277 of Table 6 are provided.

In some embodiments, the thienopyrimidine class compound is of a general formula of:

wherein Q, R1 and R2 comprises or consists of: H, an alkyl group (e.g., straight-chain alkyl (e.g., methane, ethane, propane, butane, pentane, hexane, etc.), branched alkyl group (e.g., iso-propane, 2-methyl-hexane, 3-methyl,2-propyl-octane, etc.), cycloalkyl (e.g., cyclopropane, cyclobutane, cyclopentane, cyclohexane, cyclooctane, etc.), branched cyclic alkyl (e.g., methylcyclohexane, ethylcyclobutane, propylcyclohexane, etc.)), a substituted alkyl group (e.g., halogen-substituted alkyl group (e.g., trihaloethane (e.g., trifluoroethane), halomethane (e.g., fluoromethane), dihalomethane (e.g., difluoromethane), trihalomethane (e.g., trifluoromethane), etc.), alkoxy group (e.g., ether, alcohol, etc.), alkylamine (e.g., primary amine (e.g., ethylamine, iso-butylamine, n-propylamine, sec-butylamine, iso-propylamine, iso-amylamine, methylamine, dimethylamine, n-amylamine, etc.), secondary amines (e.g., dimethylamine, methylethanolamine, diphenylamine, etc.), tertiary amine (e.g., trimethylamine, triphenylamine, etc.), thioalkyl, combinations thereof, etc.), a substituted cycloalkyl group (e.g., halogen-substituted cycloalkyl group, cycloalkoxy group, cycloalkylamine, etc.), a halogen (e.g., F, Cl, Br, I, and At), a ketone, a carbocyclic ring, an aromatic ring, a substituted aromatic ring (e.g., branched aromatic ring (e.g., ethylbenzene, methyl benzene, etc.), halobenzene (e.g., chlorobenzene, fluorobenzene, etc.)), a heterocyclic aromatic ring (e.g., comprising one or more nitrogen, oxygen and/or sulfur members which may be non-substituted or substituted with alkyl, aryl, halogen, hydrogen bond donor or acceptor), a heterocyclic non-aromatic ring (e.g., comprising carbon and one or more nitrogen, oxygen and/or sulfur members), carbocyclic or heterocyclic aromatic ring comprising carbon atoms and one or more nitrogen, oxygen and/or sulfur members fused to another aromatic ring, a multi-ring system comprising a combination of elements selected from aromatic rings, cycloalkane, heterocyclic rings, alkyl chains, and suitable C-, N-, O-, S-, and/or halogen-containing substituents, or a hydrogen bond donor or a hydrogen bond acceptor, and/or combinations thereof; and wherein Y is N or C, and wherein when Y is C the Y position may be substituted with R^(a), with R^(a) consisting of or comprising an H, alkyl (e.g., branched (e.g., isopropyl), straight chain (e.g., propyl), cycloalkyl (e.g., cyclopropyl)), heteroalkyl (e.g., methyl propyl ether), alkyl-substituted aryl (e.g., ethylbenzene), substituted alkyl (e.g., halo-substituted alkyl (e.g., trihalomethyl group (e.g., trifluoromethyl group), monohaloalkyl group (e.g. monofluoroethyl group), dihaloalkyl group (e.g. difluoroethyl group), trihaloethyl group (e.g., trifluoroethyl group), trihalopropyl (e.g., trifluoropropyl ((CH₂)₂CF₃), trihalobutyl group (e.g., trifluorobutyl group ((CH₂)₃CF₃)), trihaloisopropyl (e.g., trifluoroisopropyl), 1-fluoro,2-trifluoro, ethane, 1-trifluoro,2-ethanol), alcohol (e.g., (CH₂)_(n)OH, wherein n=0-10), alkoxy (e.g., (CH₂)_(n)—OR, wherein n=0-10, wherein R is alkyl, (CH₂)_(n)-aryl, (CH₂)_(n)-aromatic, (CH₂)_(n)-heterocycle, substituted or non-substituted aryl, aromatic or non-aromatic heterocycle with one or more N, S, O, etc.), amino (e.g., alkyl amine, amino alkyl, etc.), cyano, sulfonyl, methoxy, aldehyde, heterocycle, aromatic, combinations thereof, etc.; and wherein L is present or absent and comprises alkylene (e.g. methylene, —CH₂—, ethylene, —CH₂—CH₂—, etc) or oxalkylene (e.g. —O—, —CH₂—O—CH₂) groups.

In some embodiments, the present invention provides a composition comprising a compound having the structure of one or subscaffolds 1-6; wherein any of R1-R5, A, B, D, Q, L, W, X, Y, and Z each independently comprise organic substituents comprising fewer than 40 atoms selected from C, H, N, O, P, S, Cl, Br, F, and I. In some embodiments, the compound is selected from compounds 1-430. In some embodiments, R1 is CH₂CF₃.

In some embodiments, a compound of the present invention has a general structure of one of:

In some embodiments, all substituents (e.g., R1-R11, A, B, D, E, G, J, L, M, Q, T, X, Y, and Z) independently consist of or comprise any of the functional groups set forth herein, and in any suitable combination.

In some embodiments, R1-R11, when present on a subscaffold, each independently comprise or consist of any suitable combination of, for example: C₁-C₁₀ alkanes (e.g., straight, branched, or cyclic), halogens (e.g., Cl, Br, F, or I), OH groups (e.g., alkyl-OH), O-alkyl groups, NH₂ groups, N-dialkyl, NH-alkyl groups, CN groups, heteroalkyl groups, aromatic groups, heteroaromatic groups, a sulfone-containing group, (e.g., CH₂SO₂CH₃, CH₂SO₂NH₂, NHSO₂CH₃, NCH₃SO₂CH₃, NHSO₂NHCH₃, NHSO₂CH₂CH₃, NHSO₂(CH₂)₂NH₂, NHSO₂N(CH₃)₂, NHSO₂(CH₂)₁₋₅CH₃, and NHSO₂(CH₂)₂NHCOCH₃), S, O, or N atoms, and combinations thereof.

In some embodiments, R1-R11 are independently selected from any of the respective substituents described herein or depicted in any of Tables 1-8, in any combination. For example, in some embodiments, R1-R11, when present on a subscaffold, each independently comprise or consist of: H, alkyl group (e.g., straight-chain alkyl (e.g., methane, ethane, propane, butane, pentane, hexane, etc.), branched alkyl group (e.g., iso-propane, 2-methyl-hexane, 3-methyl,2-propyl-octane, etc.), cycloalkyl (e.g., cyclopropane, cyclobutane, cyclopentane, cyclohexane, cyclooctane, etc.), branched cyclic alkyl (e.g., methylcyclohexane, ethylcyclobutane, propylcyclohexane, etc.)), a substituted alkyl group (e.g., halogen-substituted alkyl group (e.g., mono-, di-, tetra-,penta- and trihaloethane (e.g., trifluoroethane), halomethane (e.g., fluoromethane), dihalomethane (e.g., difluoromethane), trihalomethane (e.g., trifluoromethane), etc.), alkoxy group (e.g., ether, alcohol, etc.), alkylamine (e.g., primary amine (e.g., ethylamine, iso-butylamine, n-propylamine, sec-butylamine, iso-propylamine, iso-amylamine, methylamine, dimethylamine, n-amylamine, etc.), secondary amines (e.g., dimethylamine, methylethanolamine, diphenylamine, etc.), tertiary amine (e.g., trimethylamine, triphenylamine, etc.), thioalkyl, combinations thereof, etc.), a substituted cycloalkyl group (e.g., halogen-substituted cycloalkyl group, alkyl-substituted cycloalkyl group, cycloalkoxy group, cyclolkylamine, etc.), a halogen (e.g., F, Cl, Br, I, and At), a ketone, a carbocyclic ring, an aromatic ring (e.g., heteroaryl), a substituted aromatic ring (e.g., branched aromatic ring (e.g., ethylbenzene, methyl benzene, etc.), halobenzene (e.g., chlorobenzene, fluorobenzene, etc.)), a heterocyclic aromatic ring (e.g., comprising one or more nitrogen, oxygen and/or sulfur members which may be non-substituted or substituted with alkyl, aryl, halogen, hydrogen bond donor or acceptor), a heterocyclic non-aromatic ring (e.g., comprising carbon and one or more nitrogen, oxygen and/or sulfur members), carbocyclic or heterocyclic aromatic ring comprising carbon atoms and one or more nitrogen, oxygen and/or sulfur members fused to another aromatic ring (e.g., heteroaryl), a multi-ring system comprising a combination of elements selected from aromatic rings, cycloalkane, heterocyclic rings, alkyl chains, and suitable C-, N-, O-, S-, and/or halogen-containing substituents (e.g., substituted heteroaryl), or a hydrogen bond donor or a hydrogen bond acceptor, and/or combinations thereof.

In some embodiments, A comprises or consists of: C, N, O, or S; wherein when A comprises O or S, there is no further substitution at that respective position; wherein when A comprises N or C that respective position is optionally substituted, wherein the substituent at that respective position comprises or consists of: alkyl group (e.g., straight-chain alkyl (e.g., methane, ethane, propane, butane, pentane, hexane, etc.), branched alkyl group (e.g., iso-propane, 2-methyl-hexane, 3-methyl,2-propyl-octane, etc.), cycloalkyl (e.g., cyclopropane, cyclobutane, cyclopentane, cyclohexane, cyclooctane, etc.), branched cyclic alkyl (e.g., methylcyclohexane, ethylcyclobutane, propylcyclohexane, etc.)), a substituted alkyl group (e.g., halogen-substituted alkyl group (e.g., trihaloethane (e.g., trifluoroethane), halomethane (e.g., fluoromethane), dihalomethane (e.g., difluoromethane), trihalomethane (e.g., trifluoromethane), etc.), alkoxy group (e.g., ether, alcohol, etc.), alkylamine (e.g., primary amine (e.g., ethylamine, iso-butylamine, n-propylamine, sec-butylamine, iso-propylamine, iso-amylamine, methylamine, dimethylamine, n-amylamine, etc.), secondary amines (e.g., dimethylamine, methylethanolamine, diphenylamine, etc.), tertiary amine (e.g., trimethylamine, triphenylamine, etc.), thioalkyl, combinations thereof, etc.), a substituted cycloalkyl group (e.g., halogen-substituted cycloalkyl group, cycloalkoxy group, cycloalkylamine, etc.), a halogen (e.g., F, Cl, Br, I, and At), a ketone, a carbocyclic ring, an aromatic ring, a substituted aromatic ring (e.g., branched aromatic ring (e.g., ethylbenzene, methyl benzene, etc.), halobenzene (e.g., chlorobenzene, fluorobenzene, etc.)), a heterocyclic aromatic ring (e.g., comprising one or more nitrogen, oxygen and/or sulfur members which may be non-substituted or substituted with alkyl, aryl, halogen, hydrogen bond donor or acceptor, a heterocyclic non-aromatic ring (e.g., comprising carbon and one or more nitrogen, oxygen and/or sulfur members), carbocyclic or heterocyclic aromatic ring (e.g., heteroaryl) comprising carbon atoms and one or more nitrogen, oxygen and/or sulfur members fused to another aromatic ring, a multi-ring system comprising a combination of elements selected from aromatic rings (e.g., heteroaryl), cycloalkane, heterocyclic rings, alkyl chains, and suitable C-, N-, O-, S-, and/or halogen-containing substituents, or a hydrogen bond donor or a hydrogen bond acceptor, and/or combinations thereof

In some embodiments, B comprises or consists of: C, N, O, or S; wherein when B comprises O or S, there is no further substitution at that respective position; wherein when B comprises N or C that respective position is optionally substituted, wherein the substituent at that respective position comprises or consists of: alkyl group (e.g., straight-chain alkyl (e.g., methane, ethane, propane, butane, pentane, hexane, etc.), branched alkyl group (e.g., iso-propane, 2-methyl-hexane, 3-methyl,2-propyl-octane, etc.), cycloalkyl (e.g., cyclopropane, cyclobutane, cyclopentane, cyclohexane, cyclooctane, etc.), branched cyclic alkyl (e.g., methylcyclohexane, ethylcyclobutane, propylcyclohexane, etc.)), a substituted alkyl group (e.g., halogen-substituted alkyl group (e.g., trihaloethane (e.g., trifluoroethane), halomethane (e.g., fluoromethane), dihalomethane (e.g., difluoromethane), trihalomethane (e.g., trifluoromethane), etc.), alkoxy group (e.g., ether, alcohol, etc.), alkylamine (e.g., primary amine (e.g., ethylamine, iso-butylamine, n-propylamine, sec-butylamine, iso-propylamine, iso-amylamine, methylamine, dimethylamine, n-amylamine, etc.), secondary amines (e.g., dimethylamine, methylethanolamine, diphenylamine, etc.), tertiary amine (e.g., trimethylamine, triphenylamine, etc.), thioalkyl, combinations thereof, etc.), a substituted cycloalkyl group (e.g., halogen-substituted cycloalkyl group, cycloalkoxy group, cycloalkylamine, etc.), a halogen (e.g., F, Cl, Br, I, and At), a ketone, a carbocyclic ring, an aromatic ring, a substituted aromatic ring (e.g., branched aromatic ring (e.g., ethylbenzene, methyl benzene, etc.), halobenzene (e.g., chlorobenzene, fluorobenzene, etc.)), a heterocyclic aromatic ring (e.g., comprising one or more nitrogen, oxygen and/or sulfur members which may be non-substituted or substituted with alkyl, aryl, halogen, hydrogen bond donor or acceptor, a heterocyclic non-aromatic ring (e.g., comprising carbon and one or more nitrogen, oxygen and/or sulfur members), carbocyclic or heterocyclic aromatic ring (e.g., heteroaryl) comprising carbon atoms and one or more nitrogen, oxygen and/or sulfur members fused to another aromatic ring, a multi-ring system comprising a combination of elements selected from aromatic rings (e.g., heteroaryl), cycloalkane, heterocyclic rings, alkyl chains, and suitable C-, N-, O-, S-, and/or halogen-containing substituents, or a hydrogen bond donor or a hydrogen bond acceptor, and/or combinations thereof

In some embodiments, D comprises or consists of: C, N, O, or S; wherein when D comprises O or S, there is no further substitution at that respective position; wherein D comprises N or C that respective position is optionally substituted, wherein the substituent at that respective position comprises or consists of: alkyl group (e.g., straight-chain alkyl (e.g., methane, ethane, propane, butane, pentane, hexane, etc.), branched alkyl group (e.g., iso-propane, 2-methyl-hexane, 3-methyl,2-propyl-octane, etc.), cycloalkyl (e.g., cyclopropane, cyclobutane, cyclopentane, cyclohexane, cyclooctane, etc.), branched cyclic alkyl (e.g., methylcyclohexane, ethylcyclobutane, propylcyclohexane, etc.)), a substituted alkyl group (e.g., halogen-substituted alkyl group (e.g., trihaloethane (e.g., trifluoroethane), halomethane (e.g., fluoromethane), dihalomethane (e.g., difluoromethane), trihalomethane (e.g., trifluoromethane), etc.), alkoxy group (e.g., ether, alcohol, etc.), alkylamine (e.g., primary amine (e.g., ethylamine, iso-butylamine, n-propylamine, sec-butylamine, iso-propylamine, iso-amylamine, methylamine, dimethylamine, n-amylamine, etc.), secondary amines (e.g., dimethylamine, methylethanolamine, diphenylamine, etc.), tertiary amine (e.g., trimethylamine, triphenylamine, etc.), thioalkyl, combinations thereof, etc.), a substituted cycloalkyl group (e.g., halogen-substituted cycloalkyl group, cycloalkoxy group, cycloalkylamine, etc.), a halogen (e.g., F, Cl, Br, I, and At), a ketone, a carbocyclic ring, an aromatic ring, a substituted aromatic ring (e.g., branched aromatic ring (e.g., ethylbenzene, methyl benzene, etc.), halobenzene (e.g., chlorobenzene, fluorobenzene, etc.)), a heterocyclic aromatic ring (e.g., comprising one or more nitrogen, oxygen and/or sulfur members which may be non-substituted or substituted with alkyl, aryl, halogen, hydrogen bond donor or acceptor, a heterocyclic non-aromatic ring (e.g., comprising carbon and one or more nitrogen, oxygen and/or sulfur members), carbocyclic or heterocyclic aromatic ring (e.g., heteroaryl) comprising carbon atoms and one or more nitrogen, oxygen and/or sulfur members fused to another aromatic ring, a multi-ring system comprising a combination of elements selected from aromatic rings (e.g., heteroaryl), cycloalkane, heterocyclic rings, alkyl chains, and suitable C-, N-, O-, S-, and/or halogen-containing substituents, or a hydrogen bond donor or a hydrogen bond acceptor, and/or combinations thereof.

In some embodiments, E comprises or consists of: C or N, and is optionally substituted with any suitable R6 substituent described herein.

In some embodiments, G comprises or consists of: C or N, and is optionally substituted with any suitable R6 substituent described herein.

In some embodiments, J comprises or consists of: C, N, S, or O.

In some embodiments, L is present or absent, and when present comprises or consists of: wherein L is present or absent and comprises alkylene (e.g. methylene, —CH₂—, ethylene, —CH₂—CH₂—, etc) or oxalkylene (e.g. —O—, —CH₂—O—CH₂) groups.

In some embodiments, M comprises or consists of: C, N, S, or O.

In some embodiments, Q comprises or consists of: alkyl (C₁₋₅) or heteroalkyl with one or more N, O, or S atoms.

In some embodiments, T is a: 5-membered ring comprising carbon atoms and one or more of N, S, and/or O (e.g., pyrrole, furan, thiophene imidazole, pyrazole, oxazole, isoxazole, thizole, isothiazole, triazoles, furazan, oxadiazole, thiadiazole, dithiazole, tetrazole, etc.); 6-membered ring comprising carbon atoms and one or more of N, S, and/or O (e.g., pyridine, pyran, thiopyran, diazines, oxazine, thiazine, dioxine, dithiine, triazine, tetrazine, etc.); or a cyclopropane, cyclobutane, cyclopentane, or cyclohexane. In some embodiments, any suitable R11 substitutent extends from any suitable position on the T ring.

In some embodiments, X is any suitable connector, for example an alkyl chain (e.g., (CH₂)₁₋₃), but may comprise other linear connectors, for example also comprising S, O, or N.

In some embodiments, Y comprises or consists of: O, S, N or C, and wherein when Y is N or C the Y position may be substituted with R^(a), with R^(a) consisting of or comprising an alkyl (e.g., branched (e.g., isopropyl), straight chain (e.g., propyl), cycloalkyl (e.g., cyclopropyl)), heteroalkyl (e.g., methyl propyl ether), alkyl-substituted aryl (e.g., ethylbenzene), substituted alkyl (e.g., halo-substituted alkyl (e.g., trihalomethyl group (e.g., trifluoromethyl group), monohaloalkyl group (e.g. monofluoroethyl group), dihaloalkyl group (e.g. difluoroethyl group), trihaloethyl group (e.g., trifluoroethyl group), trihalopropyl (e.g., trifluoropropyl ((CH₂)₂CF₃), trihalobutyl group (e.g., trifluorobutyl group ((CH₂)₃CF₃)), trihaloisopropyl (e.g., trifluoroisopropyl (See, e.g., compound 38)), 1-fluoro,2-trifluoro, ethane (See, e.g., compound 21), 1-trifluoro,2-ethanol (See, e.g., compound 23)), alcohol (e.g., (CH₂)_(n)OH, wherein n=0-10), alkoxy (e.g., (CH₂)_(n)—OR, wherein n=0-10, wherein R is alkyl, (CH₂)_(n)-aryl, (CH₂)_(n)-aromatic, (CH₂)_(n)-heterocycle, substituted or non-substituted aryl, aromatic or non-aromatic heterocycle with one or more N, S, O, etc.), amino (e.g., alkyl amine, amino alkyl, etc.), cyano, sulfonyl, methoxy, aldehyde, heterocycle, aromatic, combinations thereof, etc.; and wherein L is present or absent and comprises alkylene (e.g. methylene, —CH₂—, ethylene, —CH₂—CH₂—, propylene, —CH₂—CH₂—CH₂—, etc) or oxalkylene (e.g. —O—, —CH₂—O—CH₂) groups.

In some embodiments, Z comprises or consists of: H, alkyl group (e.g., straight-chain alkyl (e.g., methane, ethane, propane, butane, pentane, hexane, etc.), branched alkyl group (e.g., iso-propane, 2-methyl-hexane, 3-methyl,2-propyl-octane, etc.), cycloalkyl (e.g., cyclopropane, cyclobutane, cyclopentane, cyclohexane, cyclooctane, etc.), branched cyclic alkyl (e.g., methylcyclohexane, ethylcyclobutane, propylcyclohexane, etc.)), a substituted alkyl group (e.g., halogen-substituted alkyl group (e.g., trihaloethane (e.g., trifluoroethane), halomethane (e.g., fluoromethane), dihalomethane (e.g., difluoromethane), trihalomethane (e.g., trifluoromethane), etc.), alkoxy group (e.g., ether, alcohol, etc.), alkylamine (e.g., primary amine (e.g., ethylamine, iso-butylamine, n-propylamine, sec-butylamine, iso-propylamine, iso-amylamine, methylamine, dimethylamine, n-amylamine, etc.), secondary amines (e.g., dimethylamine, methylethanolamine, diphenylamine, etc.), tertiary amine (e.g., trimethylamine, triphenylamine, etc.), thioalkyl, a substituted cycloalkyl group (e.g., halogen-substituted cycloalkyl group, cycloalkoxy group, cycloalkylamine, etc.), a halogen (e.g., F, Cl, Br, I, and At), a ketone, a carbocyclic ring, an aromatic ring, a substituted aromatic ring (e.g., branched aromatic ring (e.g., ethylbenzene, methyl benzene, etc.), halobenzene (e.g., chlorobenzene, fluorobenzene, etc.)), a heterocyclic aromatic ring (e.g., comprising one or more nitrogen, oxygen and/or sulfur members which may be non-substituted or substituted with alkyl, aryl, halogen, hydrogen bond donor or acceptor), a heterocyclic non-aromatic ring (e.g., comprising carbon and one or more nitrogen, oxygen and/or sulfur members), carbocyclic or heterocyclic aromatic ring comprising carbon atoms and one or more nitrogen, oxygen and/or sulfur members fused to another aromatic ring, a multi-ring system comprising a combination of elements selected from aromatic rings, cycloalkane, heterocyclic rings, alkyl chains, and suitable C-, N-, O-, S-, and/or halogen-containing substituents, a hydrogen bond donor or a hydrogen bond acceptor, a sulfur-containing group (e.g., thiol, sulfide, disulfide, sulfoxide, sulfone), a group selected from CHR⁴SO₂R⁵ or NR⁴SO₂R⁵, in which R⁴ comprises or consists of: H, alkyl group (e.g., straight-chain alkyl (e.g., methane, ethane, propane, butane, pentane, hexane, etc.), branched alkyl group (e.g., iso-propane, 2-methyl-hexane, 3-methyl,2-propyl-octane, etc.), cycloalkyl (e.g., cyclopropane, cyclobutane, cyclopentane, cyclohexane, cyclooctane, etc.), branched cyclic alkyl (e.g., methylcyclohexane, ethylcyclobutane, propylcyclohexane, etc.)), a substituted alkyl group (e.g., halogen-substituted alkyl group (e.g., trihaloethane (e.g., trifluoroethane), alkylnitrile group (e.g. ethanenitryle group, CH₂CN), alkoxy group (e.g., ether, alcohol, etc.), alkylamine (e.g., primary amine (e.g., ethylamine, iso-butylamine, n-propylamine, sec-butylamine, iso-propylamine, iso-amylamine, methylamine, dimethylamine, n-amylamine, etc.), secondary amines (e.g., dimethylamine, methylethanolamine, diphenylamine, etc.), tertiary amine (e.g., trimethylamine, triphenylamine, etc.), a carbocyclic ring, a substituted cycloalkyl group (e.g., halogen-substituted cycloalkyl group, alkyl-substituted cycloalkyl group, cycloalkoxy group, cyclolkylamine, etc.) and R⁵ comprises or consists of: H, alkyl group (e.g., straight-chain alkyl (e.g., methane, ethane, propane, butane, pentane, hexane, etc.), branched alkyl group (e.g., iso-propane, 2-methyl-hexane, 3-methyl,2-propyl-octane, etc.), cycloalkyl (e.g., cyclopropane, cyclobutane, cyclopentane, cyclohexane, cyclooctane, etc.), branched cyclic alkyl (e.g., methylcyclohexane, ethylcyclobutane, propylcyclohexane, etc.)), a substituted alkyl group (e.g., halogen-substituted alkyl group (e.g., trihaloethane (e.g., trifluoroethane), halomethane (e.g., fluoromethane), dihalomethane (e.g., difluoromethane), trihalomethane (e.g., trifluoromethane), etc.), alkoxy group (e.g., ether, alcohol, etc.), alkylamine (e.g., primary amine (e.g., ethylamine, iso-butylamine, n-propylamine, sec-butylamine, iso-propylamine, iso-amylamine, methylamine, dimethylamine, n-amylamine, etc.), secondary amines (e.g., dimethylamine, methylethanolamine, diphenylamine, etc.), tertiary amine (e.g., trimethylamine, triphenylamine, etc.), thioalkyl, a substituted cycloalkyl group (e.g., halogen-substituted cycloalkyl group, cycloalkoxy group, cycloalkylamine, etc.), a ketone, a carbocyclic ring, an aromatic ring, a substituted aromatic ring (e.g., branched aromatic ring (e.g., ethylbenzene, methyl benzene, etc.), halobenzene (e.g., chlorobenzene, fluorobenzene, etc.)), a heterocyclic aromatic ring (e.g., comprising one or more nitrogen, oxygen and/or sulfur members which may be non-substituted or substituted with alkyl, aryl, halogen, hydrogen bond donor or acceptor), a heterocyclic non-aromatic ring (e.g., comprising carbon and one or more nitrogen, oxygen and/or sulfur members), carbocyclic or heterocyclic aromatic ring comprising carbon atoms and one or more nitrogen, oxygen and/or sulfur members fused to another aromatic ring, a multi-ring system comprising a combination of elements selected from aromatic rings, cycloalkane, heterocyclic rings, alkyl chains, and suitable C-, N-, O-, S-, and/or halogen-containing substituents, a hydrogen bond donor or a hydrogen bond acceptor, and/or combinations thereof, R⁵ might also be a part of the 3-8 member aromatic or non-aromatic ring comparising C, N, O, or S.

In some embodiments, the present invention provides methods for the treatment of a disease or condition comprising: administering a thienopyrimidine or thienopyridine class compound to a subject suffering from said disease or condition. In some embodiments, the thienopyrimidine or thienopyridine class compounds comprise one of subscaffolds 1-6. In some embodiments, the thienopyrimidine or thienopyridine class compounds comprise one or compound 1-430. In some embodiments, the disease or condition comprises leukemia or a solid tumor cancer (e.g., breast cancer, prostate cancer, lung cancer, liver cancer, pancreatic cancer, glioblastoma and melanoma, etc.). In some embodiments, the leukemia comprises acute leukemias, chronic leukemias, lymphoblastic leukemias, lymphocytic leukemias, myeloid leukemias, myelogenous leukemias, Acute lymphoblastic leukemia (ALL), Chronic lymphocytic leukemia (CLL), Acute myelogenous leukemia (AML), Chronic myelogenous leukemia (CML), Hairy cell leukemia (HCL), T-cell prolymphocytic leukemia (T-PLL), Large granular lymphocytic leukemia, MLL-positive leukemias, MLL-induced leukemias, MLL-rearranged leukemias, etc.

In some embodiments, the present invention provides methods of inhibiting the interaction of MLL (MLL1 and MLL2) or MLL fusion protein and menin comprising: (a) providing: (i) a sample comprising MLL (or MLL fusion proteins) and menin; and (ii) a thienopyrimidine and thienopyridine class compounds; (b) administering said composition to said sample; and (c) inhibiting the interaction between said MLL and said menin, or said MLL fusion proteins and said menin. In some embodiments, the thienopyrimidine or thienopyridine class compound comprises one of subscaffolds 1-6. In some embodiments, the thienopyrimidine or thienopyridine class compound comprises one of compound 1-430.

The compositions may comprise combinations of any of the above compounds with one another or with other compounds of interest. Stereoisomers, salts, and derivates of the compounds are further contemplated.

In some embodiments, the present invention provides a method comprising administering a composition for the treatment of leukemia (e.g., which inhibits binding of one or more MLL fusion proteins to menin or MLL wild type to menin) to a subject suffering from leukemia. In some embodiments, the leukemia comprises AML or ALL. In some embodiments, the composition comprises a thienopyrimidine or thienopyridine class compound. In some embodiments, the composition comprises a compound of the general structure of one or subscaffolds 1, 2, 3, 4, 4b, 4c, 4d, 5, or 6. In some embodiments, the composition comprises one of compounds 1-430 and/or a derivative thereof.

In some embodiments, the present invention provides a method of screening compounds effective in treating leukemia comprising assaying one or more compounds for inhibition of the interaction between MLL (or MLL fusion protein) and menin. In some embodiments, the screening is performed in vitro. In some embodiments, the screening is performed in vivo. In some embodiments, the assaying comprises a fluorescence polarization assay. In some embodiments, the assaying comprises a time-resolved fluorescence resonance energy transfer assay. In some embodiments, the assaying comprises a nuclear magnetic resonance (NMR) methods. In some embodiments, the assaying comprises cellular assays and/or animal (e.g., mice) studies.

In some embodiments, the present invention provides a method of inhibiting the interaction of MLL and menin comprising: (a) providing: (i) a sample comprising MLL and menin and (ii) a composition configured to inhibit the interaction of MLL and menin, (b) administering the composition to the sample, (c) contacting MLL and/or menin with the composition, and (d) inhibiting the interaction between MLL and menin, and between MLL fusion proteins and menin. In some embodiments, the sample comprises cells from a subject suffering from leukemia. In some embodiments, the subject is a human subject or a human patient. In some embodiments, the cells are within a subject suffering from leukemia. In some embodiments, the composition comprises a thienopyrimidine and thienopyridine class compound. In some embodiments, the present invention comprises any structural derivatives of Compounds 1-430.

In some embodiments, the present invention provides methods comprising the use of a composition and/or compound described herein (e.g., a derivative of one of Subscaffolds 1-6, one of compounds 1-430, etc.). In some embodiments, the present invention provides methods comprising the use of a composition and/or compound described herein (e.g., a derivative of one of Subscaffolds 1-6, one of compounds 1-430, etc.) for the treatment of leukemia.

In some embodiments, the present invention provides methods for the treatment of a disease or condition comprising: administering a composition described herein to a subject suffering from said disease or condition. In some embodiments, the disease or condition comprises a leukemia, hematologic malignancies, solid tumor cancer, or diabetes. In some embodiments, the leukemia comprises AML, ALL, or Mixed Lineage Leukemia.

In some embodiments, the present invention provides methods for inhibiting the interaction of menin and one or more of MLL1, MLL2, a MLL fusion protein, and a MLL Partial Tandem Duplication, comprising administering a composition described herein to the sample comprising MLL and menin.

In some embodiments, the present invention provides methods for treating disorder mediated by chromosomal rearrangement on chromosome 11 q23, comprising administering to a subject in need thereof a therapeutically effective amount of a composition described herein.

In some embodiments, the present invention provides methods for treating a disorder mediated by menin interaction with another protein, comparising administering to a subject in need thereof a therapeutically effective amount of a composition described herein.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1. Validation of direct binding of thienopyrimidine compounds to menin: a) X-ray structure of menin in complex with compound 1; b) Isothermal Titration calorimetry (ITC) for binding of compound 1 to menin.

FIG. 2. Co-Immunoprecipitation (co-IP) experiment performed in HEK293 cells transfected with MLL-AF9 demonstrating inhibition of the menin-MLL-AF9 interaction in human cells by thienopyrimidine compounds: 1, 108, 175.

FIG. 3. Thienopyrimidine compounds selectively inhibit proliferation of MLL leukemia cells as shown in MTT cell viability assay performed for compounds 1 and 108 (72 h incubation time) in MLL-AF9 transformed mouse bone marrow cells (BMC) and in E2H-HLF transformed BMC, which were used as a negative control cell line.

FIG. 4. Thienopyrimidine compounds inhibit growth of MLL-AF9 transformed BMC as demonstrated in the growth curves experiments.

FIG. 5. Growth curves experiments performed for compound 175 in MLL-AF9 transformed BMC and Hoxa9/Meis1 transformed BMC (negative control cell line), showing great selectivity of the compound towards MLL fusion protein transformed cells.

FIG. 6. Growth curves experiments performed for compound 175 in MLL-AF6 and MLL-GAS7 transformed BMC.

FIG. 7. Compound 108 reduces colony number (left) and changes morphology of colonies (right) as assessed in colony formation assay performed in MLL-AF9 BMC. Each round takes 7 days.

FIG. 8. Menin-MLL inhibitors induce differentiation in MLL-AF9 BMC as assessed by change in expression level of CD11b differentiation marker (left) and change in cell morphology (right).

FIG. 9. Differentiation induced in MLL-AF9 BMC upon treatment with Compound 175: A. Change in expression level of CD11b, B. Change in cell morphology.

FIG. 10. Menin-MLL inhibitors downregulate expression of downstream targets of MLL fusion proteins: Hoxa9 and Meis 1. A. qRT-PCR performed in MLL-AF9 BMC for Compounds 1 and 108. B. qRT-PCR performed in MLL-AF9 BMC for Compound 175.

FIG. 11. Menin-MLL inhibitors selectively inhibit growth of human MLL leukemia cell lines as shown by MTT cell viability assay performed for Compound 108 after 3 days of incubation in different human leukemia cell lines.

FIG. 12. Thienopyrimidine compounds induce apoptosis (A) and cell cycle arrest (B) in human MLL leukemia cell lines (e.g. MV4;11 with MLL-AF4 translocation).

FIG. 13. Thienopyrimidine compound 175 selectively inhibits growth of human MLL leukemia cell lines (A) and has a limited effect in non-MLL leukemia cell lines (B).

FIG. 14. Thienopyrimidine compounds downregulate expression of downstream targets of MLL fusion proteins (Hoxa9 and Meis 1) in human MLL leukemia cell lines.

FIG. 15. Thienopyrimidine compounds induce differentiation in human MLL leukemia cell lines: MV4;11 (A) and THP-1 (B).

FIG. 16. Pharmacokinetic (PK) profile of compound 108 after oral (p.o.) and intravenous (i.v.) injections of the compound to mice.

FIG. 17. MTD (Maximum Tolerated Dose) studies with compound 108 in mice after i.p. (intraperitoneal) injections of the compound.

FIG. 18. In vivo efficacy studies with compound 108 in mice model of MLL-AF9 leukemia. Increase in survival of leukemic mice was observed after once daily i.p. injections of 75 mg/kg dose.

FIG. 19. PK profile in mice for compound 175 after i.p. and oral administration of the compound.

FIG. 20. PK profile for Compound 219 after i.v. (15 mg/kg) and oral (30 mg/kg) administration of the compound.

FIG. 21. In vivo efficacy experiment with Compound 219 in BALB/c mice injected subcutaneously with MV4;11 MLL leukemia cells. Compound administered once daily via i.p. at 25 mg/kg and 35 mg/kg doses.

DEFINITIONS

The nomenclature used herein for referring to substituents is either IUPAC format or a modified format in which functional groups within a substituent are read in the order in which they branch from the scaffold or main structure. For example, in the modified nomenclature, methyl-sulfonyl-propanol refers to CH₂SO₂CH₂CH₂CH₂OH or:

As another example, according to the modified nomenclature, a methyl-amine substituent is:

while an amino-methyl substituent is:

All chemical names of substituents should be interpreted in light of IUPAC and/or the modified nomenclature and with reference to the chemical structures depicted and/or described herein.

The term “system” refers a group of objects, compounds, methods, and/or devices that form a network for performing a desired objective.

As used herein a “sample” refers to anything capable of being subjected to the compositions and methods provided herein. The sample may be in vitro or in vivo. In some embodiments, samples are “mixture” samples, which samples from more than one subject or individual. In some embodiments, the methods provided herein comprise purifying or isolating the sample. In some embodiments, the sample is purified or unpurified protein. In some embodiments, a sample may be from a clinical or research setting. In some embodiments, a sample may comprise cells, fluids (e.g. blood, urine, cytoplasm, etc.), tissues, organs, lysed cells, whole organisms, etc. In some embodiments, a sample may be derived from a subject. In some embodiments, a sample may comprise one or more partial or whole subjects.

As used herein, the term “subject” refers to any animal including, but not limited to, humans, non-human primates, bovines, equines, felines, canines, pigs, rodents (e.g., mice), and the like. The terms “subject” and “patient” may be used interchangeably, wherein the term “patient” generally refers to a human subject seeking or receiving treatment or preventative measures from a clinician or health care provider.

As used herein, the terms “subject at risk for cancer” or “subject at risk for leukemia” refer to a subject with one or more risk factors for developing cancer and/or leukemia. Risk factors include, but are not limited to, gender, age, genetic predisposition, environmental exposure, and previous incidents of cancer, preexisting non-cancer diseases, and lifestyle.

As used herein, the terms “characterizing cancer in subject” “characterizing leukemia in subject” refers to the identification of one or more properties of a cancer and/or leukemia sample in a subject, including but not limited to, the presence of benign, pre-cancerous or cancerous tissue or cells and the stage of the cancer (e.g., leukemia). Cancers (e.g., leukemia) may be characterized by identifying cancer cells with the compositions and methods of the present invention.

The terms “test compound” and “candidate compound” refer to any chemical entity, pharmaceutical, drug, and the like that is a candidate for use to treat or prevent a disease, illness, sickness, or disorder of bodily function (e.g., cancer). Test compounds comprise both known and potential therapeutic compounds. A test compound can be determined to be therapeutic by screening using the screening methods of the present invention.

As used herein, the term “effective amount” refers to the amount of a compound (e.g., a compound having a structure presented above or elsewhere described herein) sufficient to effect beneficial or desired results. An effective amount can be administered in one or more administrations, applications or dosages and is not limited to or intended to be limited to a particular formulation or administration route.

As used herein, the term “co-administration” refers to the administration of at least two agent(s) (e.g., a compound having a structure presented above or elsewhere described herein) or therapies to a subject. In some embodiments, the co-administration of two or more agents/therapies is concurrent. In other embodiments, a first agent/therapy is administered prior to a second agent/therapy. Those of skill in the art understand that the formulations and/or routes of administration of the various agents/therapies used may vary. The appropriate dosage for co-administration can be readily determined by one skilled in the art. In some embodiments, when agents/therapies are co-administered, the respective agents/therapies are administered at lower dosages than appropriate for their administration alone. Thus, co-administration is especially desirable in embodiments where the co-administration of the agents/therapies lowers the requisite dosage of a known potentially harmful (e.g., toxic) agent(s).

As used herein, the term “pharmaceutical composition” refers to the combination of an active agent with a carrier, inert or active, making the composition especially suitable for diagnostic or therapeutic use in vivo, in vivo or ex vivo.

As used herein, the term “pharmaceutically acceptable carrier” refers to any of the standard pharmaceutical carriers, such as a phosphate buffered saline solution, water, emulsions (e.g., such as an oil/water or water/oil emulsions), and various types of wetting agents. The compositions also can include stabilizers and preservatives. For examples of carriers, stabilizers and adjuvants. (See e.g., Martin, Remington's Pharmaceutical Sciences, 15th Ed., Mack Publ. Co., Easton, Pa. [1975]).

As used herein, the term “pharmaceutically acceptable salt” refers to any pharmaceutically acceptable salt (e.g., acid or base) of a compound of the present invention which, upon administration to a subject, is capable of providing a compound of this invention or an active metabolite or residue thereof. As is known to those of skill in the art, “salts” of the compounds of the present invention may be derived from inorganic or organic acids and bases. Examples of acids include, but are not limited to, hydrochloric, hydrobromic, sulfuric, nitric, perchloric, fumaric, maleic, phosphoric, glycolic, lactic, salicylic, succinic, toluene-p-sulfonic, tartaric, acetic, citric, methanesulfonic, ethanesulfonic, formic, benzoic, malonic, naphthalene-2-sulfonic, benzenesulfonic acid, and the like. Other acids, such as oxalic, while not in themselves pharmaceutically acceptable, may be employed in the preparation of salts useful as intermediates in obtaining the compounds of the invention and their pharmaceutically acceptable acid addition salts.

Examples of bases include, but are not limited to, alkali metals (e.g., sodium) hydroxides, alkaline earth metals (e.g., magnesium), hydroxides, ammonia, and compounds of formula NW₄ ⁺, wherein W is C₁₋₄ alkyl, and the like.

Examples of salts include, but are not limited to: acetate, adipate, alginate, aspartate, benzoate, benzenesulfonate, bisulfate, butyrate, citrate, camphorate, camphorsulfonate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, fumarate, flucoheptanoate, glycerophosphate, hemisulfate, heptanoate, hexanoate, hydrochloride, hydrobromide, hydroiodide, 2-hydroxyethanesulfonate, lactate, maleate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, oxalate, palmoate, pectinate, persulfate, phenylpropionate, picrate, pivalate, propionate, succinate, tartrate, thiocyanate, tosylate, undecanoate, and the like. Other examples of salts include anions of the compounds of the present invention compounded with a suitable cation such as Na⁺, NH₄ ⁺, and NW₄ ⁺ (wherein W is a C₁₋₄ alkyl group), and the like.

For therapeutic use, salts of the compounds of the present invention are contemplated as being pharmaceutically acceptable. However, salts of acids and bases that are non-pharmaceutically acceptable may also find use, for example, in the preparation or purification of a pharmaceutically acceptable compound.

As used herein, the term “instructions for administering said compound to a subject,” and grammatical equivalents thereof, includes instructions for using the compositions contained in a kit for the treatment of conditions characterized by viral infection (e.g., providing dosing, route of administration, decision trees for treating physicians for correlating patient-specific characteristics with therapeutic courses of action). The compounds of the present invention (e.g. as shown in structures above and elsewhere presented herein) can be packaged into a kit, which may include instructions for administering the compounds to a subject.

As used herein, the term “alkyl” refers to a moiety consisting of carbon and hydrogen containing no double or triple bonds. An alkyl may be linear, branched, cyclic, or a combination thereof, and may contain from one to fifty carbon atoms. Examples of alkyl groups include but are not limited to methyl, ethyl, propyl, isopropyl, cyclopropyl, butyl isomers (e.g. n-butyl, iso-butyl, tert-butyl, etc.) cyclobutyl isomers (e.g. cyclobutyl, methylcyclopropyl, etc.), pentyl isomers, cyclopentane isomers, hexyl isomers, cyclohexane isomers, and the like. Unless specified otherwise (e.g., substituted alkyl group, heteroalkyl, alkoxy group, haloalkyl, alkylamine, thioalkyl, etc.), an alkyl group contains carbon and hydrogen atoms only.

As used herein, the term “linear alkyl” refers to a chain of carbon and hydrogen atoms (e.g., ethane, propane, butane, pentane, hexane, etc.). A linear alkyl group may be referred to by the designation —(CH₂)_(q)CH₃, where q is 0-49. The designation “C₁₋₁₂ alkyl” or a similar designation, refers to alkyl having from 1 to 12 carbon atoms such as methyl, ethyl, propyl isomers (e.g. n-propyl, isopropyl, etc.), butyl isomers, cyclobutyl isomers (e.g. cyclobutyl, methylcyclopropyl, etc.), pentyl isomers, cyclopentyl isomers, hexyl isomers, cyclohexyl isomer, heptyl isomers, cycloheptyl isomers, octyl isomers, cyclooctyl isomers, nonyl isomers, cyclononyl isomers, decyl isomer, cyclodecyl isomers, etc. Similar designations refer to alkyl with a number of carbon atoms in a different range.

As used herein, the term “branched alkyl” refers to a chain of carbon and hydrogen atoms, without double or triple bonds, that contains a fork, branch, and/or split in the chain (e.g., 3,5-dimethyl-2-ethylhexane, 2-methyl-pentane, 1-methyl-cyclobutane, ortho-diethyl-cyclohexane, etc.). “Branching” refers to the divergence of a carbon chain, whereas “substitution” refers to the presence of non-carbon/non-hydrogen atoms in a moiety. Unless specified otherwise (e.g., substituted branched alkyl group, branched heteroalkyl, branched alkoxy group, branched haloalkyl, branched alkylamine, branched thioalkyl, etc.), a branched alkyl group contains carbon and hydrogen atoms only.

As used herein, the term “cycloalkyl” refers to a completely saturated mono- or multi-cyclic hydrocarbon ring system. When composed of two or more rings, the rings may be joined together in a fused, bridged or spiro-connected fashion. Cycloalkyl groups of the present application may range from three to ten carbons (C₃ to C₁₀). A cycloalkyl group may be unsubstituted, substituted, branched, and/or unbranched. Typical cycloalkyl groups include, but are not limited to, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, and the like. If substituted, the substituent(s) may be an alkyl or selected from those indicated above with regard to substitution of an alkyl group unless otherwise indicated. Unless specified otherwise (e.g., substituted cycloalkyl group, heterocyclyl, cycloalkoxy group, halocycloalkyl, cycloalkylamine, thiocycloalkyl, etc.), an alkyl group contains carbon and hydrogen atoms only.

As used herein, the term “heteroalkyl” refers to an alkyl group, as defined herein, wherein one or more carbon atoms are independently replaced by one or more heteroatoms (e.g., oxygen, sulfur, nitrogen, phosphorus, silicon, or combinations thereof). The alkyl group containing the non-carbon substitution(s) may be a linear alkyl, branched alkyl, cycloalkyl (e.g., cycloheteroalkyl), or combinations thereof. Non-carbons may be at terminal locations (e.g., 2-hexanol) or integral to an alkyl group (e.g., diethyl ether).

As used herein, the term “substituted” (e.g., substituted alyklene) means that the referenced group (e.g., alkyl, aryl, etc.) comprises a substituent group (e.g., carbon/hydrogen-only substituent, heterosubstituent, halosubstituent, etc.). The term “optionally substituted”, as used herein, means that the referenced group (e.g., alkyl, cycloalkyl, etc.) may or may not be substituted with one or more additional group(s). Substituent groups may be selected from, but are not limited to: alkyl, alkenyl, alkynyl, cycloalkyl, aryl, heteroaryl, heterocycloalkyl, hydroxyl, alkoxy, mercaptyl, cyano, halo, carbonyl, thiocarbonyl, isocyanato, thiocyanato, isothiocyanato, nitro, perhaloalkyl, perfluoroalkyl, and amino, including mono- and di-substituted amino groups, and the protected derivatives thereof. Non-limiting examples of substituents include, halo, —CN, —OR, —C(O)R, —OC(O)R, —C(O)OR, OC(O)NHR, —C(O)N(R)₂, —SR—, —S(═O)R, —S(═O)₂R, —NHR, —N(R)₂, —NHC(O)—, NHC(O)O—, —C(O)NH—, S(═O)₂NHR, —S(O)₂N(R)₂, —NHS(═O)₂, —NHS(O)₂R, C¹-C⁶alkyl, C¹-C⁶alkoxy, aryl, heteroaryl, cycloalkyl, heterocycloalkyl, halo-substituted C¹-C⁶alkyl, halo-substituted C¹-C⁶alkoxy, where each R is independently selected from H, halo, C¹-C⁶alkyl, C¹-C⁶alkoxy, aryl, heteroaryl, cycloalkyl, heterocycloalkyl, halo-substituted C¹-C⁶alkyl, halo-substituted C¹-C⁶alkoxy.

As used herein, the term “substituted alkyl” refers to an alkyl group, as defined herein, displaying one or more non-carbon-atom-containing moieties (e.g., a group containing non-carbon atoms, possibly in addition to carbon atoms). The non-carbon-atom-containing moieties atoms may comprise: oxygen, sulfur, nitrogen, phosphorus, silicon, halogens (e.g. chlorine, bromine, flourine, iodine, etc.), or combinations thereof). The non-carbon-atom-containing moieties may also comprise carbon and hydrogen. The alkyl group containing the non-carbon substitution(s) may be a linear alkyl, branched alkyl, cycloalkyl (e.g., cycloheteroalkyl), or combinations thereof. Examples of substituted alky groups include: 2-hexanol, diethyl ether (also a heteroalkyl), 1-chloro-propane, etc.

As used herein, the terms “heteroaryl” or “heteroaromatic” refer to monocyclic, bicyclic, tricyclic, and other multicyclic ring systems (e.g., having four or greater ring members), wherein at least one ring in the system is aromatic, at least one ring in the system contains one or more heteroatoms selected from nitrogen, oxygen and sulfur, and wherein each ring in the system contains 3 to 7 ring members. Unless otherwise defined herein, suitable substituents on the unsaturated carbon atom of a heteroaryl group are generally selected from halogen; —R, —OR, —SR, —NO₂, —CN, —N(R)₂, —NRC(O)R, —NRC(S)R, —NRC(O)N(R)₂, —NRC(S)N(R)₂, —NRCO₂R, —NRNRC(O)R, —NRNRC(O)N(R)₂, —NRNRCO₂R, —C(O)C(O)R, —C(O)CH₂C(O)R, —CO₂R, —C(S)R, —C(O)N(R)₂, —C(S)N(R)₂, —OC(O)N(R)₂, —OC(O)R, —C(O)N(OR)R, —C(NOR)R, —S(O)₂R, —S(O)₃R, —SO₂N(R)₂, —S(O)R, —NRSO₂N(R)₂, —NRSO₂R, —N(OR)R, —C(═NH)—N(R)₂, —P(O)₂R, —PO(R)₂, —OPO(R)₂, —(CH₂)O₂NHC(O)R, phenyl (Ph) optionally substituted with R, —O(Ph) optionally substituted with R, —(CH₂)1-2(Ph), optionally substituted with R, or —CH═CH(Ph), optionally substituted with R, wherein each independent occurrence of R is selected from hydrogen, optionally substituted C¹-C⁶alkyl, optionally substituted C¹-C⁶alkoxy, an unsubstituted 5-6 membered heteroaryl, phenyl, —O(Ph), or —CH₂(Ph), or two independent occurrences of R, on the same substituent or different substituents, taken together with the atom(s) to which each R is bound, to form an optionally substituted 3-12 membered saturated, partially unsaturated, or fully unsaturated monocyclic or bicyclic ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur. Non-limiting examples of heteroaryl groups, as used herein, include benzofuranyl, benzofurazanyl, benzoxazolyl, benzopyranyl, benzthiazolyl, benzothienyl, benzazepinyl, benzimidazolyl, benzothiopyranyl, benzo[1,3]dioxole, benzo[b]furyl, benzo[b]thienyl, cinnolinyl, furazanyl, furyl, furopyridinyl, imidazolyl, indolyl, indolizinyl, indolin-2-one, indazolyl, isoindolyl, isoquinolinyl, isoxazolyl, isothiazolyl, 1,8-naphthyridinyl, oxazolyl, oxaindolyl, oxadiazolyl, pyrazolyl, pyrrolyl, phthalazinyl, pteridinyl, purinyl, pyridyl, pyridazinyl, pyrazinyl, pyrimidinyl, quinoxalinyl, quinolinyl, quinazolinyl, 4H-quinolizinyl, thiazolyl, thiadiazolyl, thienyl, triazinyl, triazolyl and tetrazolyl. Any substituents depicted in structures or examples herein, should be viewed as suitable substituents for use in embodiments of the present invention.

As used herein, the terms “heterocycloalkyl” of “heterocycle” refer to a cycloalkyl, as defined herein, wherein one or more of the ring carbons are replaced by a moiety selected from —O—, —N═, —NR—, —C(O)—, —S(O)— or —S(O)₂—, wherein R is hydrogen, C¹-C⁸alkyl or a nitrogen protecting group, with the proviso that the ring of said group does not contain two adjacent O or S atoms. Non-limiting examples of heterocycloalkyl groups, as used herein, include morpholino, pyrrolidinyl, pyrrolidinyl-2-one, piperazinyl, piperidinyl, piperidinylone, 1,4-dioxa-8-aza-spiro[4.5]dec-8-yl, 2H-pyrrolyl, 2-pyrrolinyl, 3-pyrrolinyl, 1,3-dioxolanyl, 2-imidazolinyl, imidazolidinyl, 2-pyrazolinyl, pyrazolidinyl, 1,4-dioxanyl, 1,4-dithianyl, thiomorpholinyl, azepanyl, hexahydro-1,4-diazepinyl, tetrahydrofuranyl, dihydrofuranyl, tetrahydrothienyl, tetrahydropyranyl, dihydropyranyl, tetrahydrothiopyranyl, thioxanyl, azetidinyl, oxetanyl, thietanyl, oxepanyl, thiepanyl, 1,2,3,6-tetrahydropyridinyl, 2H-pyranyl, 4H-pyranyl, dioxanyl, 1,3-dioxolanyl, dithianyl, dithiolanyl, dihydropyranyl, dihydrothienyl, dihydrofuranyl, imidazolinyl, imidazolidinyl, 3-azabicyclo[3.1.0]hexanyl, and 3-azabicyclo[4.1.0]heptanyl.

DETAILED DESCRIPTION

The present invention provides thienopyrimidine and thienopyridine class compounds. In certain embodiments, thienopyrimidine compounds are provided for the treatment or prevention of one or more diseases or conditions (e.g., leukemia). Embodiments of the present invention directed towad the treatment and/or prevention of leukemia or recurrence thereof are described herein; however, it should be understood that the compositions and methods described herein are not limited to the leukemia application. Rather, in some embodiments, the compositions and methods described herein should be understood to also be useful for the treatment and/or prevention of other cancers, including but not limited to breast, pancreastic, prostate, liver and colon cancers, glioblastoma, diabetes etc. The compounds provided herein are not limited to therapeutic uses; any additional uses for this class of compounds are also contemplated.

In some embodiments, thienopyrimidine and thienopyridine class compounds of the present invention comprise a general formula of:

wherein W, X, Y, and R1-R4 independently comprise any suitable substituents described herein, or otherwise understood to one of skill in the art. In some embodiments, a thienopyrimidine class compound of the present invention comprises a general formula of one of:

In some embodiments, the R1-R11, A, B, D, E, G, J, L, M, Q, T, X, Y, and Z of the above structures each independently comprise or consist of one or any combination of the following moieties:

-   Single atoms: H, Cl, Br, F, or I; -   Alkanes (alkyl groups): methane (methyl), ethane (ethyl), propane     (propyl), butane (butyl), pentane (pentyl), hexane (hexyl), or any     suitable straight chain or branched C¹-C²⁰ alkane; -   Alkenes: methene, ethene, propene, butene, pentene, hexene, or any     suitable C⁷-C²⁰ alkene; -   Alkynes: methyne, ethyne, propyne, butyne, pentyne, hexyne, or any     suitable C⁷-C²⁰ alkyne; -   Cycloalkanes: cyclopropane, cyclobutane, cyclopentane, cyclohexane,     or any suitable C⁷-C²⁰ cycloalkane; -   Aromatic rings (e.g., carbon-only or heteroaromatics (e.g.,     heteroaryl)): furan, benzofuran, isobenzofuran, pyrrole, indole,     isoindole, thiophene, benzothiophene, benzo[c]thiophene, imidazole,     benzimidazole, purine, pyrazole, indazole, oxazole, benzooxazole,     isoxazole, benzisoxazole, thiazole, benzothiazole, benzene,     napthalene, pyridine, quinolone, isoquinoline, pyrazine,     quinoxaline, pyrimidine, quinazoline, pyridazine, cinnoline,     phthalazine, triazine (e.g., 1,2,3-triazine; 1,2,4-triazine; 1,3,5     triazine), thiadiazole, etc.; -   Haloalkanes: halomethane (e.g., chloromethane, bromomethane,     fluoromethane, iodomethane), di- and trihalomethane (e.g.,     trichloromethane, tribromomethane, trifluoromethane,     triiodomethane), 1-haloethane, 2-haloethane, 1,2-dihaloethane,     1-halopropane, 2-halopropane, 3-halopropane, 1,2-dihalopropane,     1,3-dihalopropane, 2,3-dihalopropane, 1,2,3-trihalopropane, and any     other suitable combinations of alkanes (or substituted alkanes) an     halogens (e.g., Cl, Br, F, I, etc.); -   Alcohols: OH, methanol, ethanol, propanol, butanol, pentanol,     hexanol, cyclic alcohols (e.g., cyclohexanol), aromatic alcohols     (e.g., phenol), or any other suitable combination of an OH moiety     with a second moiety; -   Ketones: methyl methyl ketone (acetone), methyl ethyl ketone     (butanone), propyl ethyl ketone (pentanone), or any other suitable     combination of alkyl chains with ═O; -   Aldehydes: methanol, ethanal, propanal, butanal, pentanal, hexanal,     or any other suitable combination of alkyl chain with ═O; -   Carboxylates: methanoate, ethanoate, propanote, butanoate,     pentanoate, hexanoate, or any other suitable combination of alkyl     chain with OO⁻; -   Carboxylic acids: methanoic acid, ethanoic acid, propanoic acid,     butanoic acid, pentanoic acid, hexanoic acid, or any other suitable     combination of alkyl chain with OOH; -   Ethers: methoxy, ethoxy, methylmethoxy, ethylmethoxy, or any other     suitable combination of alkyl chains surrounding an O; -   Amides: methanamide (CONH₂), ethanamide (CH₂CONH₂), propanamide     ((CH₂)₂CONH₂), alkan^(n)amide ((CH₂)_(n)CONH₂), n-methyl     alkan^(n)amide ((CH₂)—CONHCH₃), c-methyl alkan^(n)amide     ((CH₂)_(n)NHCOCH₃), n-alkyl alkan^(n)amide     ((CH₂)_(n)CONH(CH₂)_(m)CH₃), c-methyl alkan^(n)amide     OCH₂)_(n)NHCO(CH₂)_(m)CH₃), etc.; -   Primary amines: NH₂, methylamine, ethylamine, cyclopropylamine,     etc.; -   Secondary amines: aminomethyl (NHCH₃), aminoethyl (NHCH₂CH₃),     methyl-aminomethyl (CH₂NHCH₃; aka methylamine-methane),     alkyl^(n)-aminomethane ((CH₂)_(n)NHCH₃), etc.; -   Tertiary amines: dimethylamine (N(CH₃)₂), dimethylamine (N(CH₃)₂),     methyl-ethyl-amine (NCH₃CH₂CH₃), methane-diethylamine     (CH₂N(CH₂CH₃)₂; aka methylamine-diethane), etc.; -   Azides: methyl azide (CH₂NNN), ethyl azide ((CH₂)₂NNN), alkyl^(n)     azide ((CH₂)_(n)NNN), etc. -   Cyanates: methyl cyanate (CH₂OCN), ethyl cyanate ((CH₂)₂OCN),     alkyl^(n) cyanate ((CH₂)_(n)OCN), etc. -   Cyanos: cyano (—CN), methyl carbonitrile (CH₂CN), ethyl carbonitrile     ((CH₂)₂CN), alkyl^(n) carbonitrile ((CH₂)_(n)CN), etc. -   Thiols: methanethiol (CH₂SH), ethanethiol ((CH₂)₂SH),     alkan^(n)ethiol ((CH₂)_(n)SH), etc. -   Sulfides: dimethyl sulfide (CH₂SCH₃), methyl-ethyl sulfide     (CH₂SCH₂CH₃), alkyl^(n)-alkyl^(m) sulfide     ((CH₂)_(n)S(CH₂)_(m-1)CH₃), etc.; -   Sulfoxides: dimethyl sulfoxide (CH₂SOCH₃), methyl-ethyl sulfoxide     (CH₂SOCH₂CH₃), alkyl^(n)-alkyl^(m) sulfoxide     OCH₂)_(n)SO(CH₂)_(m-1)CH₃), etc.; -   Sulfone: dimethyl sulfone (CH₂SO₂CH₃; aka methyl-sulfone-methyl),     methyl-ethyl sulfone (CH₂SO₂CH₂CH₃; aka methyl-sulfone-ethyl),     alkyl^(n)-alkyl^(m) sulfone OCH₂)_(n)SO₂ (CH₂)_(m-1)CH₃; aka     alkyl^(n)-sulfone-alkyl^(m)), R^(x)SO₂R^(y) (wherein Rx and Ry are     independently selected from any of the moieties provided in this     list or combinations thereof), etc.; -   Sulfuric acids: SO₂H, methyl sulfinic acid (CH₂SO₂H), ethyl sulfinic     acid ((CH₂)₂SO₂H), sulfinic acid ((CH₂)_(n)SO₂H), etc.; -   Thiocyanate: SCN, methyl thiocyanate (CH₂SCN), ethyl thiocyanate     ((CH₂)₂SCN), alkyl^(n) thiocyanate ((CH₂)nSCN), etc.; -   Phosphates: OP(═O)(OH)₂, methyl phosphate (CH₂OP(═O)(OH)₂), ethyl     phosphate ((CH₂)₂OP(═O)(OH)₂), alkyl^(n)phosphate     ((CH₂)_(n)OP(═O)(OH)₂), etc.     In various embodiments, the above listed moieties are attached at     the X, Y, Z, A, B, D, and/or R positions in any suitable     conformation. In some embodiments, the above listed functional     groups are combined to produce the substituents depicted in     compounds 1-430 of Tables 1-8.

TABLE 1 Examples of subscaffold 1 inhibitors of menin-MLL. LC-MS com- RT, pound min. or # Structure [MH]⁺ TLC R_(f) Inhibitors with IC50 <0.1 μM  1

416.1 0.5  2

442.1 0.6 Inhibitors with IC50 0.1 μM-0.5 μM  3

427.3 1.71 min  4

399.1 1.13 min  5

437.2 2.03 min  6

581.2 2.51 min  7

469.3 2.78 min  8

469.3 2.22 min  9

399.0 1.64 min 10

455.1 0.5 11

385.5 1.42 min 12

535.2 0.6 13

487.2 0.3 14

427.1 0.5 Inhibitors with IC50 0.5 μM-2 μM 15

419.2 1.89 min 16

401.2 1.51 min 17

511.3 2.56 min 18

483.4 1.89 min 19

469.3 2.50 min 20

439.0 2.30 min 21

473.2 2.48 min 22

23

471.5 1.93 min 24

491.0 2.73 min 25

406.5 1.25 min 26

452.0 1.87 min 27

28

413.0 2.01 min 29

327.5 1.42 min 30

376.5 1.42 min 31

359.5 1.61 min 32

415.6 2.07 min 33

415.6 2.09 min 34

429.4 2.26 min 35

438.2 0.6 36

402.2 0.6 37

452.2 0.6 38

430.1 0.7 39

483.2 0.6 40

466.2 0.6 41

505.2 0.6 42

491.1 0.6 LC-MS conditions: Column type: Phenomenex Kinetex 2.6 u C18 Column dimensions: 3.0 mm × 50 mm Temperature: 60° C. Solvent A: 0.1% TFA in water Solvent B: 0.1% TFA in MeCN Gradient program: 5% to 100% B/6 min UV wavelength: 254 nm TLC conditions: Plates: Pre-coated Silica Gel 60 F₂₅₄ Developing solvent: DCM:MeOH:NH₃•H2O, 20:1:0.1

TABLE 2 Examples of subscaffold 2 of inhibitors of menin-MLL. Compound# Structure [MH]⁺ LC-MS RT, min. or TLC R_(f) Inhibitors with IC50 <0.1 μM  43

513.1 0.4  44

514.1 0.2  45

514.3 1.76 min  46

528.1 1.70 min  47

515.2 1.44 min  48

529.0 1.69 min  49

528.1 1.85 min  50

543.4 1.57 min  51

543.4 1.90 min  52

583.0 2.04 min  53

585.1 1.73 min  54

556.3 1.99 min  55

598.0 1.52 min  56

542.2 1.82 min  57

585.1 1.57 min  58

556.9 1.43 min  59

571.3 1.45 min  60

585.1 1.51 min  61

553.0 1.77 min  62

625.4 1.74 min  63

587.0 2.15 min  64

547.9 2.02 min  65

562.0 2.07 min  66

576.1 2.13 min 284

617.3 2.37 min 285

574.3 2.14 min 286

548.2 1.78 min Inhibitors with IC50 0.1 μM-0.5 μM  67

421.1 0.6  68

437.1 0.5  69

436.1 0.5  70

455.1 0.6  71

455.1 0.6  72

439.1 0.6  73

439.1 0.6  74

451.1 0.5  75

439.1 0.6  76

501.2 0.6  77

460.1 0.5  78

532.1 0.2  79

567.1 0.4  80

504.1 1.50 min  81

460.0 1.76 min  82

514.3 1.60 min  83

580.0 1.71 min  84

605.3 1.90 min  85

596.3 2.23 min Inhibitors with IC50 0.5 μM-2 μM  86

400.1 0.4  87

413.2 0.5  88

435.1 0.6  89

427.2 0.6  90

441.2 0.6  91

414.2 0.4  92

451.1 0.5  93

449.2 0.6  94

451.1 0.5  95

451.1 0.5  96

514.1 0.2  97

540.1 0.2  98

555.2 0.4  99

504.4 1.60 min 100

596.3 2.26 min 101

570.1 2.11 min 102

568.3 2.10 min 103

556.0 1.99 min 104

589.1 2.30 min 287

616.1 2.31 min

TABLE 3 Examples of subscaffold 3 of inhibitors of menin-MLL. LC-MS Com- RT, min. pound # Structure [MH]⁺ or TLC R_(f) Inhibitors with IC50 <0.1 μM 105

423.1458 0.3 106

472.31 1.46 min Inhibitors with IC50 0.1 μM-0.5 μM 107

453.1 1.25 min 108

407.5 1.72 min 109

423.1 1.31 min 110

437.2 1.32 min 111

439.3 1.28 min 112

437.2 1.31 min 113

422.2 1.61 min 114

423.2 1.30 min 115

526.3 1.59 min 116

504.1 1.47 min 117

421.0 1.55 min 118

435.4 2.06 min 119

441.1 1.76 min 120

435.5 1.59 min 121

436.3 1.12 min 122

457.3 1.65 min 123

422.1618 0.2 124

512.2093 0.4 125

466.1885 0.1 126

420.7 1.47 min 127

465.2 0.1 128

481.1 0.1 129

451.1 0.3 130

464.2 1.32 min 131

396.1 1.25 min 132

413.5 1.37 min 133

413.5 1.37 min 134

396.1459 0.3 135

433.3 1.62 min Inhibitors with IC50 0.5 μM-2 μM 136

476.2 1.35 min 137

436.3 1.05 min 138

433.3 1.15 min 139

422.2 1.01 min 140

437.2 1.16 min 141

473.2 1.57 min 142

520.3 1.41 min 143

519.4 1.28 144

145

146

475.0 1.72 min 147

421.3 1.95 min 148

475.0 1.54 min 149

367.0 1.29 min 150

381.5 1.42 min 151

381.5 1.46 min 152

447.0 1.44 min 153

381.5 1.42 min 154

155

403.6 1.35 min 156

486.4 1.49 min 157

422.1629 0.3 158

434.1630 0.2 159

472.3 1.51 min

TABLE 4 Examples of subscaffold 3 and 4 of inhibitors of menin-MLL. LC-MS RT, min. Com- or TLC pound # Structure [MH]⁺ R_(f) Inhibitors with IC50 <0.1 μM 160

486.1676 0.2 161

597.2367 0.2 162

540.2159 0.3 163

501.1 1.91 min 164

501.1 1.94 min 288

661.2677 0.1 289

594.2057 0.1 Inhibitors with IC50 0.1 μM-0.5 μM 165

423.1458 0.2 166

422.1625 0.2 167

512.2095 0.3 168

526.2243 0.3 169

504.2400 0.3 170

533.2310 0.3 171

518.2557 0.3 172

583.2127 0.3 173

583.2133 0.3 174

512.1974 0.3

TABLE 5 Examples of subscaffold 4 of inhibitors of menin-MLL. LC-MS Com- RT, min. pound # Structure [MH]⁺ or TLC R_(f) Inhibitors with IC50 <0.1 μM 175

471.1579 0.3 176

489.1485 0.3 177

499.1891 0.4 178

525.2052 0.4 179

515.1828 0.2 180

501.1684 0.3 181

501.1675 0.3 182

487.1519 0.3 183

501.1678 0.2 184

489.4 1.60 min 185

551.2 1.23 min 186

514.1998 0.1 187

545.1951 0.2 188

545.1941 0.2 189

528.1783 0.2 190

559.2098 0.2 191

559.2096 0.2 192

584.2415 015 193

558.123 0.1 194

542.5 1.33 min 195

552.4 1.55 min 196

565.3 1.63 min 197

510.4 1.65 min 198

553.6 1.63 min 199

551.8 1.65 min 200

568.3 1.73 min 201

582.1 1.80 min 202

551.2 1.55 min 203

565.3 1.31 min 204

552.4 1.52 min 205

546.1 1.48 min 206

471.1576 0.4 207

566.5 1.53 min 208

556.0 1.46 min 209

566.2 1.52 min 210

564.4 1.43 min 211

501.1 1.77 min 212

541.9 1.82 min 213

546.1690 0.1 214

546.1693 0.1 215

515.1835 0.2 216

572.2050 0.1 217

589.2204 0.1 218

485.2 2.10 min 219

485.2 2.02 min 220

546.4 1.86 min 221

559.0 1.82 min 222

585.1 1.72 min 223

581.2 2.12 min 224

505.1181 0.3 225

562.1400 0.1 226

579.1552 0.1 290

501.1 1.60 min 291

568.3 1.65 min 292

587.3 1.86 min 293

511.6 1.92 min 294

500.2 1.37 min 295

499.3 2.00 min 296

515.2 1.82 min 297

595.4 1.94 min 298

551.2 2.01 min 299

529.0 1.64 min 300

559.0 1.57 min 301

542.2 1.56 min 302

601.4 1.94 min 303

580.3 1.73 min 304

580.3 1.65 min 305

521.2 1.75 min 306

591.5 1.96 min 307

606.5 1.78 min 308

601.4 1.92 min 309

565.3 1.74 min 310

578.5 1.64 min 311

566.5 1.69 min 312

621.5 2.12 min 313

667.4 2.14 min 314

633.5 1.96 min 315

647.6 2.00 min 316

603.5 1.95 min 317

671.6 2.45 min 318

649.4 2.38 min 319

647.6 2.12 min 320

641.3 2.48 min 321

544.9 1.51 min 322

597.2 1.75 min 323

596.3 1.83 min 324

565.3 1.74 min 325

558.1 1.38 min 326

582.4 1.83 min 327

580.3 1.69 min 328

590.6 1.46 min 329

596.6 1.49 min 330

579.4 1.47 min 331

567.4 1.58 min 332

565.6 1.35 min 333

644.6 1.46 min 334

581.2 1.71 min 335

581.2 1.60 min 336

597.5 1.44 min 337

611.6 1.53 min 338

615.5 1.93 min 339

735.5 2.24 min 340

715.4 1.91 min 341

729.5 2.01 min 342

721.4 1.97 min 343

721.4 2.06 min 344

693.5 1.91 min 345

656.3 1.54 min 346

669.5 2.29 min 347

672.5 1.73 min 348

655.4 2.19 min 349

565.3 1.43 min 350

579.4 1.48 min 351

579.4 1.47 min 352

579.4 1.63 min 353

566.5 1.83 min 354

591.5 1.70 min 355

611.3 1.57 min 356

625.4 1.55 min 357

639.5 1.57 min 358

627.5 1.46 min 359

598.4 1.60 min 360

614.3 1.53 min 361

566.2 1.74 min 362

628.4 1.43 min 363

640.4 1.45 min 364

654.5 1.46 min 365

579.4 1.85 min 366

596.3 1.55 min 367

611.3 1.49 min 368

646.4 1.80 min 369

611.6 1.52 min 370

638.3 1.89 min 371

644.6 1.70 min 372

641.3 1.60 min 373

654.5 1.72 min 374

579.1 1.64 min 375

704.3 1.75 min 376

668.6 1.63 min 377

674.3 2.11 min 378

665.3 1.73 min 379

579.4 1.95 min 380

472.3 1.55 min 381

585.1554 0.2 382

567.1893 0.2 383

515.1837 0.3 384

501.1674 0.2 385

572.2047 0.1 386

559.3001 0.1 387

545.1943 0.1 388

581.2050 0.1 389

595.2214 0.1 390

581.2056 0.1 391

582.2001 0.1 392

596.2159 0.1 393

583.2570 0.1 394

639.2833 0.2 395

593.1615 0.2 396

653.2995 0.2 397

707.3461 0.2 398

721.3622 0.2 399

639.3203 0.2 400

639.2837 0.2 401

653.2989 0.2 402

598.2566 0.3 403

675.2503 0.2 404

689.2663 0.2 405

690.2613 0.2 406

625.2682 0.2 407

676.2457 0.1 423

449.1915 0.2 424

472.3 1.65 min 425

641.3 2.29 min 426

612.5 1.63 min 427

582.4 1.64 min 428

596.3 1.60 min 429

612.5 1.67 min 430

582.4 1.60 min Inhibitors with IC50 0.1 μM-0.5 μM 227

446.2 1.53 min 228

471.1584 0.3 229

471.1579 0.3 230

486.1675 0.2 231

500.1844 0.3 232

489.1685 0.2 233

486.1679 0.3 234

489.1483 0.3 235

487.1517 0.3 236

524.8 1.45 min 237

559.3 1.57 min 238

584.2 1.52 min 239

556.3 1.52 min 240

553.3 1.52 min 241

580.3 1.81 min 242

476.1729 0.2 243

446.2 1.52 min 244

515.2 1.98 min 245

489.1 1.96 min 246

546.1 1.77 min 247

542.1945 0.1 408

537.1 1.87 min 409

571.9 1.78 min 410

485.5 1.66 min 411

667.4 2.23 min 412

635.3 2.32 min 413

685.7 2.55 min 414

649.4 2.46 min 415

663.5 2.53 min 416

678.5 2.68 min 417

485.1732 0.3 Inhibitors with IC50 0.5 μM-2 μM 248

473.2 1.47 min 249

472.3 1.39 min 250

463.3 1.14 251

586.4 1.27 min 252

485.1735 0.3

TABLE 6 Examples of subscaffold 5 of inhibitors of menin-MLL. LC-MS Com- RT, pound min. # Structure [MH]⁺ or R_(f) Inhibitors with IC50 0.1 μM-0.5 μM 253

534.1 1.20 min 254

489.1 1.63 min 255

504.4 1.52 min 256

480.1 1.65 min 257

485.2 1.67 min 258

435.4 1.49 min 259

540.4 1.57 min 260

455.2 1.54 min 261

455.2 1.59 min 262

500.2 1.45 min 263

446.2 1.62 min Inhibitors with IC50 0.5 μM-2 μM 264

502.3 1.77 min 265

450.4 1.09 min 266

451.3 1.15 min 267

533.5 1.26 min 268

523.6 1.68 min 269

523.3 2.00 min 270

463.0 1.76 min 271

505.3 1.70 min 272

520.3 1.19 min 273

451.3 1.50 min 274

489.5 1.49 min 275

435.4 1.79 min 276

489.5 1.58 min 277

421.0 1.27 min

TABLE 7 Examples of subscaffold 3 and 4 of inhibitors of menin-MLL. LC-MS RT, min. or Compound# Structure [MH]⁺ TLC R_(f) Inhibitors with IC50 <0.1 μM 278

500.2 1.45 min 279

431.2 1.78 min 280

436.0 1.19 min Inhibitors with IC50 0.1 μM-0.5 μM 281

450.1 1.30 min Inhibitors with IC50 0.5 μM-2 μM 282

366.3 1.35 min 418

596.6 2.03 min 419

610.4 2.15 min 420

580.0 1.49 min 421

582.4 1.94 min

TABLE 8 Examples of subscaffold 6 of inhibitors of menin-MLL. Com- LC-MS pound RT, min. # Structure [MH]⁺ or TLC R_(f) 283

422

487.1883 0.3 In other embodiments, additional substituents, not depicted in Tables 1-8 or described herein by name or formula, are formed by combination of the above functional groups; such substituents are within the scope of the present invention, and may be appended to one or more of subscaffolds 1-6 to yield compositions within the scope of the present invention.

Subscaffolds 1-6 are provided herein as exemplary subscaffolds of the general thienopyrimidine and thienopyridine class of compounds. While these subscaffolds, with any combination of the substituents depicted or described herein (e.g., explicitly or through combination of functional groups), are within the scope of embodiments of the invention, the present invention is not limited to such subscaffolds. Thienopyrimidine and thienopyridine derivatives of subscaffolds 1-6 are also within the scope of embodiments of the present invention. Substitutions and/or addition/deletion of substituents of subscaffolds 1-6 that produce functional equivalents and/or improved functionality (e.g., enhanced therapeutic effect, enhanced bioavailability, improved human tolerance, reduced side effects, etc.) are also within the scope of embodiments of the present invention.

In some embodiments, the present invention provides compositions and methods for prevention and/or treatment of leukemia (e.g. MLL-related leukemia and other acute leukemias). In some embodiments, the present invention provides compositions and method for the inhibition of the protein-protein interaction between menin and MLL fusion proteins and/or menin and MLL wild type proteins (both MLL1 and MLL2). In some embodiments, compositions and methods inhibit the interaction that is important for the oncogenic (e.g. leukemogenic) potential of MLL fusions. In some embodiments, the present invention provides small molecule inhibitors of interactions between menin and MLL fusion proteins and/or menin and MLL wild type proteins (both MLL1 and MLL2). In some embodiments, compositions and methods reverse (e.g. inhibit, decrease, abolish, etc.) the oncogenic (e.g. leukemogenic) potential of MLL fusion proteins. In some embodiments, compositions find utility in targeted therapies (e.g. anti-leukemia agents). In some embodiments, compounds block menin-MLL interactions.

In some embodiments, the present invention provides compositions which inhibit the interaction between MLL (e.g. MLL fusion proteins and MLL wild type proteins, both MLL1 and MLL2) and menin. In some embodiments, any compounds, small molecules (e.g. pharmaceuticals, drugs, drug-like molecules, etc.), macromolecules (e.g. peptides, nucleic acids, etc.) and/or macromolecular complexes which inhibit the MLL-menin interaction find utility in the present invention. In some embodiments, the present invention provides small molecule compounds which inhibit MLL-menin interactions. In some embodiments, compositions of the present invention decrease the affinity of menin for MLL (e.g. MLL fusion proteins) and/or MLL (e.g. MLL wild type proteins, both MLL1 and MLL2) for menin. In some embodiments, compositions of the present invention disrupt bonding (e.g. hydrogen bonding, ionic bonding, covalent bonding, etc.), molecular interactions (e.g. hydrophobic interactions, electrostatic interactions, van der Waals interactions, etc.), shape recognition, and/or molecular recognition between MLL (e.g. MLL fusion proteins or MLL wild type protein) and menin. However, an understanding of the mechanisms of action is not required to practice the invention and the invention is not limited to any particular mechanism of action.

The present invention provides any small molecules or classes of small molecules which disrupt, target, or inhibit MLL/menin interactions; and/or treat/prevent leukemia. In some embodiments, small molecules are effective in inhibiting the interaction of MLL-fusion proteins with menin or MLL wild type protein with menin. In particular embodiments, the present invention provides thienopyrimidine and thienopyridine classes of small molecules. In some embodiments, thienopyrimidine small molecules of the present invention inhibit the interaction of MLL (e.g. MLL-fusion proteins or MLL wild type, both MLL1 and MLL2) with menin. In some embodiments, thienopyrimidine and thienopyridine small molecules of the present invention inhibit the oncogenic (e.g. leukemogenic) effects of MLL-fusion proteins, and/or MLL-menin and MLL fusion protein-menin interactions. In some embodiments, thienopyrimidine and thienopyridine small molecules of the present invention treat and/or prevent leukemia (e.g. MLL-dependant leukemias, MLL-related leukemias, or other leukemias with and without high level of HOX genes expression etc.).

In some embodiments, the present invention provides administration of compositions of the present invention to subjects (e.g. leukemia patients) to treat or prevent disease (e.g. cancer, leukemia, MLL-related leukemia, etc.). In some embodiments, the present invention provides administration of compositions for the treatment or prevention of leukemia (e.g. acute leukemias, chronic leukemias, lymphoblastic leukemias, lymphocytic leukemias, myeloid leukemias, myelogenous leukemias, Acute lymphoblastic leukemia (ALL), Chronic lymphocytic leukemia (CLL), Acute myelogenous leukemia (AML), Chronic myelogenous leukemia (CML), Hairy cell leukemia (HCL), T-cell prolymphocytic leukemia (T-PLL), Large granular lymphocytic leukemia, MLL-positive leukemias, MLL-induced lukemias, etc.).

In some embodiments, any of the above compounds is co-administered or used in combination with a known therapeutic agent (e.g., methotrexate, 6-mercaptopurine, antibody therapies, etc.). In some embodiments, a compound of the present invention is co-administered with another therapeutic agent effective in treating one or more leukemias.

In some embodiments, a compound of the present invention is co-administered with one or more therapeutic agents approved for the treatment of Acute Lymphoblastic Leukemia (ALL), for example: ABITREXATE (Methotrexate), ADRIAMYCIN PFS (Doxorubicin Hydrochloride), ADRIAMYCIN RDF (Doxorubicin Hydrochloride), ARRANON (Nelarabine), Asparaginase Erwinia chrysanthemi, CERUBIDINE (Daunorubicin Hydrochloride), CLAFEN (Cyclophosphamide), CLOFARABINE, CLOFAREX (Clofarabine), CLOLAR (Clofarabine), Cyclophosphamide, Cytarabine, CYTOSAR-U (Cytarabine), CYTOXAN (Cyclophosphamide), Dasatinib, Daunorubicin Hydrochloride, Doxorubicin Hydrochloride, Erwinaze (Asparaginase Erwinia Chrysanthemi), FOLEX (Methotrexate), FOLEX PFS (Methotrexate), GLEEVEC (Imatinib Mesylate), ICLUSIG (Ponatinib Hydrochloride), Imatinib Mesylate, MARQIBO (Vincristine Sulfate Liposome), Methotrexate, METHOTREXATE LPF (Methorexate), MEXATE (Methotrexate), MEXATE-AQ (Methotrexate), Nelarabine, NEOSAR (Cyclophosphamide), ONCASPAR (Pegaspargase), Pegaspargase, Ponatinib Hydrochloride, RUBIDOMYCIN (Daunorubicin Hydrochloride), SPRYCEL (Dasatinib), TARABINE PFS (Cytarabine), VINCASAR PFS (Vincristine Sulfate), Vincristine Sulfate, etc.

In some embodiments, a compound of the present invention is co-administered with one or more therapeutic agents approved for the treatment of Acute Myeloid Leukemia (AML), for example: ADRIAMYCIN PFS (Doxorubicin Hydrochloride), ADRIAMYCIN RDF (Doxorubicin Hydrochloride), Arsenic Trioxide, CERUBIDINE (Daunorubicin Hydrochloride), CLAFEN (Cyclophosphamide), Cyclophosphamide, Cytarabine, CYTOSAR-U (Cytarabine), CYTOXAN (Cyclophosphamide), Daunorubicin Hydrochloride, Doxorubicin Hydrochloride, NEOSAR (Cyclophosphamide), RUBIDOMYCIN (Daunorubicin Hydrochloride), TARABINE PFS (Cytarabine), TRISENOX (Arsenic Trioxide), VINCASAR PFS (Vincristine Sulfate), Vincristine Sulfate, etc.

In some embodiments, a compound of the present invention is co-administered with one or more therapeutic agents approved for the treatment of Chronic Lymphocytic Leukemia (CLL), for example: Alemtuzumab, AMBOCHLORIN (Chlorambucil), AMBOCLORIN (Chlorambucil), ARZERRA (Ofatumumab), Bendamustine Hydrochloride, CAMPATH (Alemtuzumab), CHLORAMBUCILCLAFEN (Cyclophosphamide), Cyclophosphamide, CYTOXAN (Cyclophosphamide), FLUDARA (Fludarabine Phosphate), Fludarabine Phosphate, LEUKERAN (Chlorambucil), LINFOLIZIN (Chlorambucil), NEOSAR (Cyclophosphamide), Ofatumumab, TREANDA (Bendamustine Hydrochloride), etc.

In some embodiments, a compound of the present invention is co-administered with one or more therapeutic agents approved for the treatment of Chronic Myelogenous Leukemia (CML), for example: BOSULIF (Bosutinib), Bosutinib, CLAFEN (Cyclophosphamide), Cyclophosphamide, Cytarabine, CYTOSAR-U (Cytarabine), CYTOXAN (Cyclophosphamide), Dasatinib, GLEEVEC (Imatinib Mesylate), ICLUSIG (Ponatinib Hydrochloride), Imatinib Mesylate, NEOSAR (Cyclophosphamide), Nilotinib, Omacetaxine Mepesuccinate, Ponatinib Hydrochloride, SPRYCEL (Dasatinib), SYNRIBO (Omacetaxine Mepesuccinate), TARABINE PFS (Cytarabine), TASIGNA (Nilotinib), etc.

In some embodiments, a compound of the present invention is co-administered with one or more therapeutic agents approved for the treatment of Meningeal Leukemia, for example: CYTARABINE, CYTOSAR-U (Cytarabine), TARABINE PFS (Cytarabine), etc.

In some embodiments, the compositions of the present invention are provided as pharmaceutical and/or therapeutic compositions. The pharmaceutical and/or therapeutic compositions of the present invention can be administered in a number of ways depending upon whether local or systemic treatment is desired and upon the area to be treated. Administration can be topical (including ophthalmic and to mucous membranes including vaginal and rectal delivery), pulmonary (e.g., by inhalation or insufflation of powders or aerosols, including by nebulizer; intratracheal, intranasal, epidermal and transdermal), oral or parenteral. Parenteral administration includes intravenous, intraarterial, subcutaneous, intraperitoneal or intramuscular injection or infusion; or intracranial, e.g., intrathecal or intraventricular, administration. Compositions and formulations for topical administration can include transdermal patches, ointments, lotions, creams, gels, drops, suppositories, sprays, liquids and powders. Conventional carriers; aqueous, powder, or oily bases; thickeners; and the like can be necessary or desirable. Compositions and formulations for oral administration include powders or granules, suspensions or solutions in water or non aqueous media, capsules, sachets or tablets. Thickeners, flavoring agents, diluents, emulsifiers, dispersing aids or binders can be desirable. Compositions and formulations for parenteral, intrathecal or intraventricular administration can include sterile aqueous solutions that can also contain buffers, diluents and other suitable additives such as, but not limited to, penetration enhancers, carrier compounds and other pharmaceutically acceptable carriers or excipients. Pharmaceutical and/or therapeutic compositions of the present invention include, but are not limited to, solutions, emulsions, and liposome containing formulations. These compositions can be generated from a variety of components that include, but are not limited to, preformed liquids, self emulsifying solids and self emulsifying semisolids.

The pharmaceutical and/or therapeutic formulations of the present invention, which can conveniently be presented in unit dosage form, can be prepared according to conventional techniques well known in the pharmaceutical/nutriceutical industries. Such techniques include the step of bringing into association the active ingredients with the pharmaceutical carrier(s) or excipient(s). In general the formulations are prepared by uniformly and intimately bringing into association the active ingredients with liquid carriers or finely divided solid carriers or both, and then, if necessary, shaping the product. The compositions of the present invention can be formulated into any of many possible dosage forms such as, but not limited to, tablets, capsules, liquid syrups, soft gels, suppositories, and enemas. The compositions of the present invention can also be formulated as suspensions in aqueous, non aqueous, oil-based, or mixed media. Suspensions can further contain substances that increase the viscosity of the suspension including, for example, sodium carboxymethylcellulose, sorbitol and/or dextran. The suspension can also contain stabilizers. In one embodiment of the present invention the pharmaceutical compositions can be formulated and used as foams. Pharmaceutical foams include formulations such as, but not limited to, emulsions, microemulsions, creams, jellies and liposomes. While basically similar in nature these formulations vary in the components and the consistency of the final product.

Dosing and administration regimes are tailored by the clinician, or others skilled in the pharmacological arts, based upon well known pharmacological and therapeutic considerations including, but not limited to, the desired level of therapeutic effect, and the practical level of therapeutic effect obtainable. Generally, it is advisable to follow well-known pharmacological principles for administrating chemotherapeutic agents (e.g., it is generally advisable to not change dosages by more than 50% at time and no more than every 3-4 agent half-lives). For compositions that have relatively little or no dose-related toxicity considerations, and where maximum efficacy is desired, doses in excess of the average required dose are not uncommon. This approach to dosing is commonly referred to as the “maximal dose” strategy. In certain embodiments, the compounds are administered to a subject at a dose of about 0.01 mg/kg to about 200 mg/kg, more preferably at about 0.1 mg/kg to about 100 mg/kg, even more preferably at about 0.5 mg/kg to about 50 mg/kg. When the compounds described herein are co-administered with another agent (e.g., as sensitizing agents), the effective amount may be less than when the agent is used alone. Dosing may be once per day or multiple times per day for one or more consecutive days.

EXPERIMENTAL Example 1 General Methods of Compounds Synthesis

Compounds of subscaffold 1 can be prepared according to the following general method (Scheme 1 and 2).

Compounds of subscaffold 2 can be prepared according to the following general method (Scheme 3 and 4).

Compounds of subscaffold 3 can be prepared according to the following general method (Scheme 5 and 6).

Compounds of subscaffold 4 can be prepared according to the following general method (Scheme 7, 8 and 9).

Compounds of subscaffold 5 can be prepared according to the following general method (Scheme 10 and 11).

Compounds of subscaffold 6 can be prepared according to the following general method (Scheme 12 and 13).

Example 1 Representative Procedure for the Synthesis of Compounds from Subscaffold 1

4,4,4-trifluorobuteraldehyde 5 g (39.6 mmol), cyanoacetamide 3.36 g (39.6 mmol) and sulfur 1.28 g (39.6 mmol) was stirred in 40 mL of DMF in the presence of 6.7 mL of triethylamine for 24 hs. Solvent was evaporated under reduced pressure and the residue was loaded on silica gel column and eluted with pure ethyl acetate to afford 8.4 g of 2-amino-5-(2,2,2-trifluoroethyl)thiophene-3-carboxamide. ¹H NMR CDCl₃ (300 MHz): 7.97 (s, 1H), 6.76 (s, 1H), 3.59 (br, 2H), 3.35 (q, 2H, J 10.3 Hz), 2.98 (s, 1H), 2.88 (s, 1H). ¹³C NMR CDCl₃ (75 MHz): 168.6, 125.6, 124.3, 111.7, 107.3, 36.8, 34.7 (q, J 31.4 Hz).

8.4 g of 2-amino-5-(2,2,2-trifluoroethyl)thiophene-3-carboxamide was refluxed in a mixture of 28 mL of triethylorthoformate and 20 mL of acetic acid for 4 hs. Solvents were removed under reduced pressure and the residue was triturated hexane-ethyl acetate mixture (1:1). The solid was filtered off to afford 5.7 g of 6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4(3H)-one. ¹H NMR MeOH-d4 (300 MHz): 12.6 (br, 1H), 8.14 (s, 1H), 7.42 (s, 1H), 4.07 (q, 2H, J 11.0 Hz). ¹³C NMR MeOH-d4 (75 MHz): 164.5, 157.01, 146.1, 128.4, 124.6, 123.5, 33.6 (q, J 31.5 Hz).

5.7 g of 6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4(3H)-one was added to 16 mL of POCl₃ with one drop of DMF. The heterogeneous mixture was refluxed for 3 hs and then evaporated.

The residue was quenched with ice and saturated ammonia solution and extracted with chloroform. Combined extracts were evaporated with silica gel and loaded on a short silica gel column. The column was eluted with hexane-ethyl acetate (5:1) to afford 5.9 g of 4-chloro-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidine. ¹H NMR CDCl₃ (300 MHz): 8.86 (s, 1H), 7.39 (s, 1H), 3.76 (q, 2H, J 9.9 Hz). ¹³C NMR CDCl₃ (75 MHz): 169.0, 154.7, 153.2, 129.9, 125.3, 123.5, 121.3, 35.9 (q, J 33.0 Hz).

0.5 g of 3-isothiocyanato-2-methylprop-1-ene was added to dropwise via syringe to a solution of 1-Bocpiperazine in 5 mL of ethanol. The mixture was stirred for 1.5 hs at RT and then evaporated. The residue was washed several times with diethyl ether to produce 1.1 g of white solid intermediate, which was dissolved in 3 mL of conc. HCl and heated in the pressure tube at 100 degrees for 1.5 hours. Cooled solution was quenched with ammonia solution and extracted with ethyl acetate. Combined organic layers were washed with brine, dried over MgSO₄ and evaporated to afford pure 382 mg of 5,5-dimethyl-2-(piperazin-1-yl)-2,5-dihydrothiazole, which was use as is in the next step. ¹H NMR (400 MHz, CDCl3): δ 1.53 (6H, s), 2.96 (4H, t, J=5 Hz), 3.49 (4H, t, J=5 Hz), 3.73 (2H, s). ¹³C NMR (100 MHz, CDCl3): δC 28.83 (2C), 45.76 (2C), 49.34 (2C), 59.52, 73.30, 164.16; mp 67° C. −70° C.; Mass spec (ES+): m/z 199.2 (M⁺+1).

A solution of 0.5 g of 4-chloro-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidine (2.4 mmol), 0.56 g of 5,5-dimethyl-2-(piperazin-1-yl)-2,5-dihydrothiazole (2.8 mmol), and 0.91 g of N,N-diisopropylethylamine (7.1 mmol) in 20 mL of THF was refluxed for 6 h. After cooling, the mixture was partitioned between ethyl acetate and H₂O. The combined organic extracts were washed with brine, dried over MgSO₄ and concentrated to a pale yellow solid. Purification by silica gel column chromatography using dichloromethane/methanol (97:3) as eluent gave 0.82 g of 4-(4-(5,5-dimethyl-4,5-dihydrothiazol-2-yl)piperazin-1-yl)-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidine (compound 1) as a pale yellow solid. Its monohydrochloride salt was obtained by adding 1 equivalent of 1N HCl solution in diethyl ether to a solution of compound in ethanol. ¹H NMR (400 MHz DMSO-d6): δ 8.46 (s, 1H), 7.70 (s, 1H), 4.37 (s, 1H), 4.09 (m, 4H), 3.81, (m, 4H), 3.45 (q, 2H, J=10.1 Hz), 1.61 (s, 6H). ESI MS [MH⁺]: 416.1.

Example 2 Representative Procedure for the Synthesis of Compounds from Subscaffold 2

To a solution of 2 g of 4-(bromomethyl)phenyl acetic acid in 20 mL of methanol was added 0.2 mL of TMSCl and mixture was stirred for 2 hrs. The solvent was removed in vacuo and residue was twice redissolved in MeOH and reconcentrated to give desired product, which was used in the xet step without purification. Bromoester was refluxed in 50 mL of water in the presence of 2.5 g of sodium bisulfilte for 3 hs. After cooling down the precipitate was filtered off and dried on the funnel overnight. The solid was suspended in 15 mL of POCl₃ and 1 g of PCl₅ was slowly added to a suspension. The mixture stirred for 3 hs at RT. A mixture was concentrated and 10 mL of conc. ammonia in water was slowly added to 0° C., redissolved compound in 30 mL of acetonitrile. After stirring for 12 hs at RT, a mixture was concentrated, partitioned between ethyl acetate and saturated sodium carbonate solution. Organic layer was washed with brine, dried over MgSO₄ and evaporated. The intermediate ester was dissolved in 5 mL of EtOH and 10 ml of 10M NaOH was added. The mixture was stirred for 24 hs and then concentrated. Acidification with 12M HCl resulted in precipitate. 2-(4-(sulfamoylmethyl)phenyl)acetic acid was filtered off and dried overnight. Used without purification in the next step.

190 mg of 4-chloro-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidine (0.75 mmol) was added to a stirred solution of 290 mg of N,N-diisopropylethylamine (2.25 mmol) and 168 mg of 1-Boc-piperazine (0.9 mmol) in 20 mL and was heated at reflux overnight. Solvent was removed under reduced pressure and the residue was loaded on silica gel column. Elution with DCM:MeOH produced 215 mg of Boc-intermediate as a pale yellow solid. Later it was dissolved in 20 mL of 4M HCl in dioxane and stirred for 2 hs. Solvent was evaporated under reduced pressure and the residue was partitioned between ethyl acetate and saturated sodium carbonate solution. Organic layer was washed with brine, dried over MgSO₄ and evaporated to afford 150 mg of 4-(piperazin-1-yl)-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidine, which was used in the next step without purification.

23 mg of 2-(4-(sulfamoylmethyl)phenyl)acetic acid (0.1 mmol), 20 mg of 4-(piperazin-1-yl)-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidine (0.067 mmol), 20 mg of EDCI (0.1 mmol) and 4 mg of DMAP (0.033 mmol) was stirred in 2 mL of DCM. After 2 hs reaction mixture was concentrated and residue was loaded on silica gel column. Elution with DCM-MeOH 9:1 and evaporation of fraction produced 38 mg of (4-(2-oxo-2-(4-(6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl)piperazin-1-yl)ethyl)phenyl)methanesulfonamide (compound 44). ¹H NMR (400 MHz, CDCl3): δ 8.44 (s, 1H), 7.36 (d, 2H, J=8 Hz), 7.25 (d, 2H, J=8 Hz), 7.20 (s, 1H), 4.88 (s, 2H), 4.26 (s, 1H), 3.5-4.0 (m, 10H). ESI MS [MH⁺]: 514.1. Its monohydrochloride salt was obtained by adding 1 equivalent of 1N HCl solution in diethyl ether to a solution of compound in ethanol.

Example 3 Representative Procedure for the Synthesis of Compounds from Subscaffold 3

4.8 g of 4-chloro-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidine (19 mmol) was added to a stirred solution of 7.4 g of N,N-diisopropylethylamine (57 mmol) and 4.56 g of 4-amino-N-Boc-piperidine (22.8 mmol) in 95 mL and was heated at reflux overnight. On the morning reaction mixture was evaporated with silica gel and loaded on the column. The product was eluted with hexane-ethyl acetate from 1:1 to 1:5 yielding 7.42 g of boc-derivative. Boc-intermediate was dissolved in 40 mL of 4M HCl in dioxane and stirred for 2 hs. Solvent was evaporated under reduced pressure and the residue was partitioned between ethyl acetate and saturated sodium carbonate solution. Organic layer was washed with brine, dried over MgSO₄ and evaporated to afford 5.3 g of N-(piperidin-4-yl)-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-amine, which was used in later steps without purification. ¹H NMR (600 MHz, CDCl3): δ 8.47 (s, 1H), 7.13 (s, 1H), 5.32 (d, 1H, J=7.7 Hz), 4.32 (m, 1H), 3.64 (q, 2H, 10 Hz), 3.19 (m, 2H), 2.83 (m, 2H), 2.57 (br, 1H), 2.14 (m, 2H), 1.55 (m, 2H). ¹³C NMR (150 MHz, CDCl3): δC 166.85, 155.96, 154.33, 128.12, 126.62, 118.66, 116.48, 47.98, 45.32, 35.56 (q, J=31.5 Hz), 33.10. ESI MS [MH⁺]: 317.2.

59 mg of N-(piperidin-4-yl)-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-amine (0.19 mmol) and 21 mg of p-hydroxybenzaldehyde (0.19 mmol) were dissolved in 0.5 mL of MeOH in the presence of 10 ukL of acetic acid. 19 mg of NaBH₃CN (0.3 mmol) was slowly added to that mixture and solution was stirred for 24 hs. All volatiles were removed under reduced pressure and residue was partitioned between water and ethyl acetate. Organic layer was washed with brine, dried over magnesium sulfate and evaporated. The residue was purified on silica gel column with DCM:MeOH:Et3N as eluent resulting in 62 mg of 4-((4-((6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl)amino)piperidin-1-yl)methyl)phenol (compound 105). ¹H NMR (600 MHz, CDCl3): δ 8.46 (s, 1H), 7.09 (d, 2H, J=8.4 Hz), 7.07 (s, 1H), 6.68 (d, 2H, J=8.4 Hz), 5.28 (d, 1H, J=7.7 Hz), 4.21 (m, 1H), 3.59 (q, 2H, 9.9 Hz), 3.46 (s, 2H), 2.96 (m, 2H), 2.21 (m, 2H), 2.09 (m, 2H), 1.62 (m, 2H). ¹³C NMR (150 MHz, CDCl3): δC 166.45, 156.08, 155.98, 154.14, 131.01, 128.23, 125.57, 118.65, 116.52, 115.62, 62.48, 52.10, 47.96, 35.50 (q, J=31.5 Hz), 31.89. ESI MS [MH⁺]: 423.1458. Its monohydrochloride salt was obtained by adding 1 equivalent of 1N HCl solution in diethyl ether to a solution of compound in ethanol.

Example 4 Analytical Data for Selected Compounds from Subscaffold 3 and 4 and Representative Procedures for their Synthesis

Synthesized according to this synthetic route:

Monohydrochloride salt exists as a mixture of rotomers in approximate ratio 10:1, NMR is described for the major one: ¹H NMR (600 MHz, CD₃OD): δ 8.41 (s, 1H), 7.76 (s, 1H), 7.62 (m, 2H), 7.57 (d, 1H, J=8.3 Hz), 7.33 (s, 1H), 4.57 (m, 1H), 4.05 (m, 1H), 3.96 (m, 1H), 3.91 (q, 2H, J=10.3 Hz), 3.53 (m, 1H), 3.42 (m, 1H), 3.22 (m, 1H), 2.60 (m, 2H), 2.16 (m, 1H), 2.04 (m, 1H). ¹³C NMR (150 MHz, CD₃OD): δC 167.34, 158.35, 154.49, 138.61, 130.12, 128.67, 127.53, 127.29, 125.19, 121.45, 118.12, 114.51, 113.72, 112.03, 111.14, 53.12, 52.61, 51.47, 51.22, 50.34, 49.41, 35.46 (q, J=33 Hz), 30.32. ESI MS [MH⁺]: 486.1676.

Synthesized according to this synthetic route:

Monohydrochloride salt exists as a mixture of rotomers in approximate ratio 10:1, NMR is described for the major one: ¹H NMR (600 MHz, CD₃OD): δ 9.34 (s, 1H), 8.39 (s, 1H), 7.72 (s, 1H), 7.59 (m, 2H), 7.53 (d, 1H, J=8.3 Hz), 7.29 (s, 1H), 4.51 (m, 1H), 4.02 (m, 1H), 3.91 (m, 1H), 3.88 (q, 2H, J=10.3 Hz), 3.54 (m, 2H), 3.51 (m, 1H), 3.41 (m, 2H), 3.19 (m, 1H), 2.98 (m, 2H), 2.59 (m, 2H), 2.12 (m, 1H), 2.03 (m, 1H), 1.97 (m, 2H), 1.85 (m, 1H), 1.83 (m, 1H). ¹³C NMR (150 MHz, CD₃OD): δC 168.29, 164.2, 157.42, 154.41, 139.41, 131.32, 128.62, 127.41, 127.05, 124.49, 121.42, 117.12, 113.94, 113.45, 111.97, 111.21, 63.11, 53.31, 52.59, 51.42, 51.13, 50.48, 48.31, 48.21, 47.97, 35.48 (q, J=33 Hz), 30.21, 28.71, 26.33. ESI MS [MH⁺]: 597.2367.

Synthesized according to this synthetic route:

Monohydrochloride salt exists as a mixture of rotomers in approximate ratio 10:1, NMR is described for the major one: ¹H NMR (600 MHz, CD₃OD): δ 8.39 (s, 1H), 7.74 (s, 1H), 7.61 (m, 2H), 7.52 (d, 1H, J=8.3 Hz), 7.27 (s, 1H), 4.54 (m, 1H), 4.24 (m, 2H), 4.03 (m, 1H), 3.94 (m, 1H), 3.88 (q, 2H, J=10.3 Hz), 3.51 (m, 1H), 3.37 (m, 1H), 3.21 (m, 1H), 2.58 (m, 2H), 2.16 (m, 1H), 2.03 (m, 1H), 1.28 (m, 1H), 0.59 (m, 2H), 0.48 (m, 2H). ¹³C NMR (150 MHz, CD₃OD): δC 167.24, 158.39, 154.62, 138.67, 130.19, 128.64, 127.62, 127.38, 125.55, 121.75, 118.37, 114.53, 113.85, 112.07, 111.07, 62.75, 53.33, 52.73, 51.39, 51.25, 50.52, 49.43, 35.52 (q, J=33 Hz), 31.23, 12.50, 4.18. ESI MS [MH⁺]: 540.2159.

2.4 mL of benzyl bromide (20 mmol) was added dropwise over an hour to a solution of 1.6 mL of pyridine in 5 mL of acetonitrile. Then reaction mixture was heated at 70 to 72° C. for 3 hours. Solvent was removed under reduced pressure and the residue was dissolved in 16 mL of ethanol. 1.1 g of sodium borohydride (30 mmol) was added in small portions over 30 minutes. After stirring for 24 hs reaction mixture was carefully quenched with 50 mL of water and solvents were removed in vacuo. The residue was portioned between ethyl acetate and 2M NaOH solution. Organic extracts were washed with brine, dried over MgSO₄ and evaporated to afford crude 3.36 g of crude 1-benzyl-1,2,3,6-tetrahydropyridine which was used in the next step without purification.

3.36 g of 1-benzyl-1,2,3,6-tetrahydropyridine (0.19 mmol) was dissolved in 35 mL of water containing 1.5 mL of trifluoroacetic acid (0.2 mmol). To that solution 5.87 g of NBS was added in small portions. After 4 hs reaction mixture was transferred to 50 mL of 20% NaOH solution and stirred overnight. On the morning reaction mixture was extracted with dichloromethane and combined organic fractions were dried over sodium sulfate and concentrated. The residue was purified on silica gel column using hexane-ethyl acetate 3:1 as eluent. Evaporation of solvent produced 1.2 g of 3-benzyl-7-oxa-3-azabicyclo[4.1.0]heptane as colorless oil.

A solution of 1.2 g of 3-benzyl-7-oxa-3-azabicyclo[4.1.0]heptane (6.3 mmol) was refluxed in the presence of 0.62 g of sodium azide (9.5 mmol) and 3 g of lithium perchlorate (19 mmol) for 4 hs. After completion reaction mixture was evaporated and the residue was extracted with dichloromethane, washed with water and combined organic fractions were dried over sodium sulfate and concentrated. The residue was purified on silica gel column using hexane-ethyl acetate 4:1 as eluent affording 980 mg of trans-4-azido-1-benzylpiperidin-3-ol.

201 mg of trans-4-azido-1-benzylpiperidin-3-ol (0.87 mmol) was dissolved in 3 ml of EtOH-water 3:1. To that solution 77 mg of zinc (12 mmol), 112 mg of ammonium chloride (2.1 mmol) were added and heterogeneous mixture was refluxed for 10 minutes. After cooling down reaction mixture was diluted with 8 mL of ethyl acetate and 0.5 mL of conc. ammonia in water, filtered off. Organic layer washed with brine, dried over sodium sulfate and evaporated. The residue was purified on silica gel column using DCM:MeOH 10:1 as eluent affording 120 mg of trans-4-amino-1-benzylpiperidin-3-ol.

The mixture of 36.7 mg of trans-4-amino-1-benzylpiperidin-3-ol (0.18 mmol), 30 mg of 4-chloro-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidine (0.12 mmol) and 46 mg of N,N-diisopropylethylamine (0.36 mmol) was refluxed in 0.75 mL of isopropanol for 18 hs. Then reaction mixture was concentrated and purified on silica gel column eluting with DCM:MeOH 20:1 to afford 45 mf of trans-1-benzyl-4-((6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl)amino)piperidin-3-ol (Compound 163). Its monohydrochloride salt was obtained by adding 1 equivalent of 1N HCl solution in diethyl ether to a solution of compound in ethanol. ¹H NMR (600 MHz, CD₃OD) of HCl salt, signals are all broadened because of intramolecular H-bond: δ 8.37 (1H), 7.51-7.60 (6H), 4.43 (4H), 4.12 (1H), 3.85 (2H), 3.55 (2H), 3.21 (1H), 2.99 (1H), 2.06 (1H). ¹³C NMR (150 MHz, CD₃OD): δC 165.78, 158.45, 153.97, 132.59, 131.46, 130.51, 130.18, 127.45, 125.62, 122.09, 118.50, 68.02, 61.86, 56.88, 54.15, 52.38, 35.81 (q, J=31.5 Hz), 28.14. ESI MS [MH⁺]: 423.1458.

Monohydrochloride salt exists as a mixture of rotomers in approximate ratio 10:1, NMR is described for the major one: ¹H NMR (600 MHz, CD₃OD): δ 8.69 (s, 1H), 7.87 (s, 1H), 7.66 (m, 2H), 7.55 (m, 3H), 7.44 (m, 2H) m 7.34 (m, 2H), 5.13 (m, 1H), 4.53 (m, 3H), 4.35 (m, 2H), 4.07 (m, 1H), 3.99 (q, 2H, J=10.3 Hz), 3.75 (m, 1H), 3.63 (m, 1H), 3.42 (m, 1H), 2.41 (m, 2H). ¹³C NMR (150 MHz, CD₃OD): δC 159.23, 158.93, 151.86, 132.75, 132.67, 132.65, 131.70, 130.59, 129.75, 129.20, 127.37, 125.54, 122.78, 119.37, 4095, 38.63, 35.33 (q, J=33 Hz), 33.39, 33.25, 33.15, 25.98, 25.97. ESI MS [MH⁺]: 512.2095.

Example 5 Analytical Data for Selected Compounds from Subscaffold 4 and Representative Procedures for their Synthesis

A mixture of 0.5 g of 5-methylindole-2-carboxylic acid, 0.25 mL of thionyl chloride, 5 mL of chloroform and small drop of DMF was refluxed for 2 hs. The reaction mixture was cooled to RT, poured into a mixture of 5 g of ice and 5 mL of 25% ammonia solution, and then stirred for 2 hs. The precipitated product was filtered off, washed with water and dried to yield 350 mg of 5-methylindole-2-carboxamide. ¹H NMR (600 MHz, DMSO-d6): δ 11.37 (s, 1H), 7.89 (br, 1H), 7.36 (s, 1H), 7.30 (d, 1H, J=8.4 Hz), 7.28 (br, 1H), 7.02 (s, 1H), 6.99, (d, 1H, J=8.4 Hz), 2.36 (s, 3H). ¹³C NMR (150 MHz, CDCl3): δC 160.95, 132.95, 129.77, 126.15, 125.44, 123.10, 118.77, 110.02, 100.65, 19.20.

A mixture of 340 mg of 5-methylindole-2-carboxamide (1.95 mmol), 1.5 g of phosphorus oxychloride (9.75) and 8 mL of chloroform was refluxed for 2 hs. Then cooled solution was poured into 20 mL of water and stirred for 1 hr. After separation the organic layer was dried over sodium sulfate and concentrated. The residue was purified on silica gel column using hexane-ethyl acetate 5:1 to afford 245 mg of 5-methyl-1H-indole-2-carbonitrile. ¹H NMR (600 MHz, CDCl3): δ 8.61 (br, 1H), 7.44 (s, 1H), 7.30 (d, 1H, J=8.4 Hz), 7.21 (d, 1H, J=8.4 Hz), 7.11 (s, 1H), 2.44 (s, 3H). ¹³C NMR (150 MHz, CDCl3): δC 135.34, 131.25, 128.28, 126.53, 121.33, 114.41, 113.95, 111.39, 106.11, 21.36.

To a solution of 245 mg of 5-methyl-1H-indole-2-carbonitrile (1.6 mmol) in 5 mL of acetonitrile 0.434 mL of di-tert-butyl dicarbonate (1.9 mmol) and 29 mg of DMAP (0.24 mmol) were added and stirred at room temperature for 30 min. The solvent was removed in vacuo, and the resultant crude product was purified by column chromatography (silica gel) using pure hexane-ethyl acetate 10:1 as an eluant to afford 334 mg of tert-butyl 2-cyano-5-methyl-1H-indole-1-carboxylate. ¹H NMR (600 MHz, CDCl3): δ 8.10 (d, 1H, J=8.8 Hz), 7.39 (s, 1H), 7.31 (d, 1H, J=8.8 Hz), 7.26 (s, 1H), 2.45 (s, 3H), 1.72, (s, 9H). ¹³C NMR (150 MHz, CDCl3): δC 148.22, 134.94, 133.78, 129.85, 121.61, 121.24, 115.53, 113.46, 108.76, 85.54, 28.05, 21.21.

To a stirred solution of 334 mg of tert-butyl 2-cyano-5-methyl-1H-indole-1-carboxylate (1.3 mmol) in carbon tetrachloride (5 mL) was added 232 mg of N-bromosuccinimide (1.3 mmol) and 11 mg of AIBN (0.065 mmol). The mixture was refluxed for 1 h, then cooled and concentrated, and the residues were purified by chromatography on silica gel using hexane-ethyl acetate 20:1 to give 340 mg of tert-butyl 2-cyano-5-bromomethyl-1H-indole-1-carboxylate. ¹H NMR (600 MHz, CDCl3): δ 8.22 (d, 1H, J=8.8 Hz), 7.64 (s, 1H), 7.53 (d, 1H, J=8.8 Hz), 7.31 (s, 1H), 4.60 (s, 2H), 1.73, (s, 9H). ¹³C NMR (150 MHz, CDCl3): δC 147.64, 136.27, 133.92, 129.34, 127.45, 122.33, 121.15, 116.46, 113.02, 109.75, 87.14, 33.23, 28.01.

16.7 mg of tert-butyl 2-cyano-5-bromomethyl-1H-indole-1-carboxylate (0.05 mmol) and 15.8 mg of N-(piperidin-4-yl)-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-amine (0.05 mmol) were dissolved in 0.6 mL of DCM. 12.9 mg of DIPEA (0.1 mmol) was added to that solution and reaction mixture was stirred for 18 hs. Then reaction mixture was directly loaded on silica gel column and the product was eluted with DCM-MeOH 30:1. After evaporation of solvent boc-protected intermediate was dissolved in 0.5 mL of ACN and 0.06 mL of SnCl₄ (0.5 mmol) was added. The homogenous reaction mixture was stirred for 1 h and then all volatiles were removed in vacuo. The residue was quenched ammonia and extracted with ethyl acetate. Combined organic fractions were dried over MgSO₄ and concentrated. The residue was purified on silica gel column using hexane-ethyl acetate-MeOH 1:1:0.1 to produce 16 mg of 5-((4-((6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl)amino)piperidin-1-yl)methyl)-1H-indole-2-carbonitrile (Compound 175). Its monohydrochloride salt was obtained by adding 1 equivalent of 1N HCl solution in diethyl ether to a solution of compound in ethanol. The hydrochloride salt was recrystallized from methanol. ¹H NMR (600 MHz, DMSO-d6): δ 12.62 (s, 1H), 10.74 (br, 1H), 8.33 (s, 1H), 8.07 (d, 1H, J=7 Hz), 7.93, s, 1H), 7.70 (s, 1H), 7.62 (d, 1H, J=12 Hz), 7.56 (d, 1H, J=12 Hz), 7.45 (s, 1H), 4.36 (s, 1H), 4.30 (m, 1H), 4.03 (q, 2H, J=11 Hz), 3.41 (m, 2H), 3.11 (m, 2H), 2.12 (m, 2H), 1.98 (m, 2H).

¹³C NMR (150 MHz, DMSO-d6): δC 165.88, 155.72, 153.78, 137.18, 128.42, 126.97, 125.78, 125.37, 124.52, 122.22, 121.31, 116.12, 114.22, 113.36, 112.54, 106.84, 59.27, 50.36, 45.46, 33.73 (q, J=33 Hz), 28.23. ESI MS [MH⁺]: 471.1579.

Monohydrochloride salt exists as a mixture of rotomers in approximate ratio 10:1, NMR is described for the major one: ¹H NMR (600 MHz, MeOD-d4): 8.68 (s, 1H), 7.94 (s, 1H), 7.82 (s, 1H), 7.69 (d, 1H, J=8.4 Hz), 7.62 (d, 1H, J=8.4 Hz), 7.35 (s, 1H), 4.63 (m, 1H), 4.48 (s, 2H), 4.45 (q, 2H, J=7.2 Hz), 3.99 (q, 2H, J=10.3 Hz), 3.63 (m, 2H), 3.26 (m, 2H), 2.34 (m, 2H), 2.14 (m, 2H), 1.45 (t, 3H, 7.2 Hz). ¹³C NMR (150 MHz, MeOD-d4): δC 149.93, 138.83, 132.93, 129.40, 127.94, 127.30, 127.26, 125.43, 123.06, 122.70, 118.69, 114.30, 113.86, 112.75, 112.60, 111.75, 62.02, 52.39, 48.39, 41.53, 35.22 (q, J=33 Hz), 29.53, 15.76. ESI MS [MH⁺]: 499.1891.

Monohydrochloride salt exists as a mixture of rotomers in approximate ratio 10:1, NMR is described for the major one: ¹H NMR (600 MHz, MeOD-d4): 8.40 (s, 1H), 7.94 (s, 1H), 7.72 (d, 1H, J=8.8 Hz), 7.61 (d, 1H, J=8.8 Hz), 7.59 (s, 1H), 7.35 (s, 1H), 4.48 (m, 3H), 4.27 (m, 2H), 4.88 (q, 2H, J=10.6 Hz), 3.61 (m, 2H), 3.25 (m, 2H), 2.34 (m, 2H), 2.02 (m, 2H), 1.30 (m, 1H), 0.58 (m, 2H), 0.50 (m, 2H). ¹³C NMR (150 MHz, MeOD-d4): δC 164.91, 157.63, 153.86, 139.38, 130.60, 129.39, 127.91, 127.49, 127.17, 125.66, 123.22, 121.97, 118.29, 114.36, 112.89, 112.18, 61.96, 52.69, 50.85, 47.34, 35.54 (q, J=33 Hz), 29.95, 12.65, 4.38. ESI MS [MH⁺]: 525.2052.

Monohydrochloride salt exists as a mixture of rotomers in approximate ratio 10:1, NMR is described for the major one: ¹H NMR (600 MHz, MeOD-d4): 8.75 (s, 1H), 7.96 (s, 1H), 7.88 (d, 1H, J=8.8 Hz), 7.74 (d, 1H, J=8.8 Hz), 7.64 (s, 1H), 7.37 (s, 1H), 4.67 (m, 1H), 4.51 (m, 3H), 4.03 (q, 2H, J=10.6 Hz), 3.93 (m, 2H), 3.65 (m, 2H), 3.30 (m, 2H), 2.36 (m, 2H), 2.18 (m, 2H). ¹³C NMR (150 MHz, MeOD-d4): δC 164.91, 139.70, 133.26, 129.21, 127.95, 127.11, 127.10, 125.48, 123.11, 122.84, 122.79, 118.74, 114.21, 113.09, 112.99, 61.95, 61.79, 52.29, 49.60, 48.54, 35.12 (q, J=33 Hz),29.45. ESI MS [MH⁺]: 515.1828.

To the mixture of 2.46 g of 2-methoxy-3-methylanisaldehyde (16 mmol) and 4.72 g of methyl azidoacetate (41 mmol) in 20 mL of MeOH is added 7.6 mL of 5.4M MeONa over 30 minute at −10 degrees. After addition the mixture was stirred for additional hour at the same temperature and then transferred in cold room (4 degrees) and stirred overnight. On the morning reaction mixture was poured in 0.5 L mixture of ice and conc. ammonium chloride solution, stirred for 10 minutes and filtered off. The solid was washed with plenty of ice cold water and then moved at ambient temperature. After air drying for 1 hr the solid was dissolved in 50 mL of DCM, dried over magnesium sulfate and passed through short silica gel plug. Evaporation of solvent produced 3.5 g of methyl 2-azido-3-(2-methoxy-3-methylphenyl)acrylate, that was used in the next step without further purification.

4.16 g of methyl 2-azido-3-(2-methoxy-3-methylphenyl)acrylate (16.8 mmol) was dissolved in 20 mL of toluene. 560 mg of rhodium (II) trifluoroacetate dimer (0.84 mmol) was added and the reaction mixture was heated at 50 degrees for 24 hs. Then solvent was evaporated and residue was loaded on silica gel column and eluted with hexane-ethyl acetate 10:1 to produce after evaporation 1.3 g of methyl 4-methoxy-5-methyl-1H-indole-2-carboxylate. ¹H NMR (600 MHz, CDCl₃): δ 9.05 (br, 1H), 7.32 (s, 1H), 7.11 (d, 1H, J=8 Hz), 7.04 (d, 1H, J=8 Hz), 4.03 (s, 3H), 3.94 (s, 1H), 2.33 (s, 1H).

80 mg of methyl 4-methoxy-5-methyl-1H-indole-2-carboxylate (0.39 mmol) was heated at 80 degrees in a sealed tube with 1 mL of 7M ammonia in methanol. After one week reaction the solvent evaporated to produce 79 mg of 4-methoxy-5-methyl-1H-indole-2-carboxamide that was used without purification in the next step.

A mixture of 79 mg of 4-methoxy-5-methyl-1H-indole-2-carboxamide (0.39 mmol), 0.19 mL of phosphorus oxychloride (2 mmol) and 1.5 mL of chloroform was refluxed for 2 hs. Then cooled solution was poured into 10 mL of water and stirred for 1 hr. After separation the organic layer was dried over sodium sulfate and concentrated. The residue was purified on silica gel column using hexane-ethyl acetate 5:1 to afford 51 mg of 4-methoxy-5-methyl-1H-indole-2-carbonitrile.

To a solution of 390 mg of 4-methoxy-5-methyl-1H-indole-2-carbonitrile 2.1 mmol) in 7 mL of acetonitrile 0.574 mL of di-tert-butyl dicarbonate (0.74 mmol) and 25 mg of DMAP (0.21 mmol) were added and stirred at room temperature for 30 min. The solvent was removed in vacuo, and the resultant crude product was purified by column chromatography (silica gel) using hexane-ethyl acetate 10:1 as an eluent to afford 561 mg of tert-butyl 2-cyano-4-methoxy-5-methyl-1H-indole-1-carboxy late.

To a stirred solution of 561 mg of tert-butyl 2-cyano-4-methoxy-5-methyl-1H-indole-1-carboxylate (1.96 mmol) in carbon tetrachloride (9 mL) was added 349 mg of N-bromosuccinimide (1.96 mmol) and 64 mg of AIBN (0.39 mmol). The mixture was refluxed for 1 h, then cooled and concentrated and filtered through short silica gel plug using hexane-ethyl acetate 10:1 to give 852 mg of crude tert-butyl 5-(bromomethyl)-2-cyano-4-methoxy-1H-indole-1-carboxylate that was used in the next step without further purification.

852 mg of crude ten-butyl 2-cyano-5-bromomethyl-1H-indole-1-carboxylate (1.96 mmol) and 829 mg of N-(piperidin-4-yl)-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-amine (2.62 mmol) were dissolved in 5 mL of DCM. 1.3 mL of DIPEA (7.5 mmol) was added to that solution and reaction mixture was stirred for 18 hs. Then reaction mixture was directly loaded on silica gel column and the product was eluted with Hexane-Ethyl acetate-MeOH 2:1:0.1. After evaporation of solvent boc-protected intermediate was dissolved in 14 mL of ACN and 1.7 mL of SnCl₄ (0.5 mmol) was added. The homogenous reaction mixture was stirred for 1 h and then all volatiles were removed in vacuo. The residue was quenched ammonia and extracted with ethyl acetate. Combined organic fractions were dried over MgSO₄ and concentrated. The residue was purified on silica gel column using hexane-ethyl acetate-MeOH 1:1:0.2 to produce 494 mg of 4-methoxy-5-((4-((6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl)amino)piperidin-1-yl)methyl)-1H-indole-2-carbonitrile (Compound 180). Its monohydrochloride salt was obtained by adding 1 equivalent of 1N HCl solution in diethyl ether to a solution of compound in ethanol. Monohydrochloride salt exists as a mixture of rotomers in approximate ratio 10:1, NMR is described for the major one: ¹H NMR (600 MHz, MeOD-d4): δ 8.71 (s, 1H), 7.85 (s, 1H), 7.60 (s, 1H), 7.45 (d, 1H, J=8 Hz), 7.23 (d, 1H, J=8 Hz), 4.63 (m, 1H), 4.46 (s, 2H), 4.29 (s, 3H), 4.01 (q, 2H, J=10.5 Hz), 3.64 (m, 2H), 3.29 (m, 2H), 2.33 (m, 2H), 2.13 (m, 2H). ¹³C NMR (150 MHz, MeOD-d4): δC 155.08, 149.56, 142.48, 133.14, 130.79, 130.44, 127.31, 123.36, 122.79, 118.72, 118.60, 114.63, 113.09, 110.78, 107.95, 108.25, 61.21, 56.92, 52.45, 35.11 (q, J=33 Hz), 29.50. ESI MS [MH⁺]: 501.1684.

To the mixture of 6.59 g of 3-methylanisaldehyde (44 mmol) and 12.65 g of methyl azidoacetate (110 mmol) in 60 mL of MeOH is added 20 mL of 5.4M MeONa over 30 minute at −10 degrees. After addition the mixture was stirred for additional hour at the same temperature and then transferred in cold room (4 degrees) and stirred overnight. On the morning reaction mixture was poured in 1 L mixture of ice and conc. ammonium chloride solution, stirred for 10 minutes and filtered off. The solid was washed with plenty of ice cold water and then moved at ambient temperature. After air drying for 1 hr the solid was dissolved in 50 mL of DCM, dried over magnesium sulfate and passed through short silica gel plug. Evaporation of solvent produced 9.8 g of methyl 2-azido-3-(4-methoxy-3-methylphenyl)acrylate, that was used in the next step without further purification.

250 mg of 2-azido-3-(4-methoxy-3-methylphenyl)acrylate (1 mmol) was dissolved in 1 mL of toluene. 30 mg of rhodium (II) trifluoroacetate dimer (0.045 mmol) was added and the reaction mixture was heated at 50 degrees for 24 hs. Then solvent was evaporated and residue was loaded on silica gel column and eluted with hexane-ethyl acetate 10:1 to produce after evaporation 125 mg of methyl 6-methoxy-5-methyl-1H-indole-2-carboxylate. ¹H NMR (600 MHz, CDCl₃): δ 8.73 (br, 1H), 7.39 (s, 1H), 7.10 (s, 1H), 6.77 (s, 1H), 3.92 (s, 3H), 3.88 (s, 1H), 2.28 (s, 1H).

200 mg of methyl 6-methoxy-5-methyl-1H-indole-2-carboxylate (1 mmol) was heated at 80 degrees in a sealed tube with 2 mL of 7M ammonia in methanol. After one week reaction the solvent evaporated to produce 202 mg of 6-methoxy-5-methyl-1H-indole-2-carboxamide that was used without purification in the next step.

A mixture of 202 mg of 6-methoxy-5-methyl-1H-indole-2-carboxamide (1 mmol), 0.47 mL of phosphorus oxychloride (5 mmol) and 3 mL of chloroform was refluxed for 2 hs. Then cooled solution was poured into 10 mL of water and stirred for 1 hr. After separation the organic layer was dried over sodium sulfate and concentrated. The residue was purified on silica gel column using hexane-ethyl acetate 5:1 to afford 116 mg of 6-methoxy-5-methyl-1H-indole-2-carbonitrile. ¹H NMR (600 MHz, CDCl₃): δ 8.26 (br, 1H), 7.37 (s, 1H), 7.06 (s, 1H), 6.76 (s, 1H), 3.88 (s, 1H), 2.28 (s, 3H).

To a solution of 116 mg of 6-methoxy-5-methyl-1H-indole-2-carbonitrile (0.62 mmol) in 2 ml, of acetonitrile 0.171 mL of di-tert-butyl dicarbonate (0.74 mmol) and 20 mg of DMAP (0.24 mmol) were added and stirred at room temperature for 30 min. The solvent was removed in vacuo, and the resultant crude product was purified by column chromatography (silica gel) using hexane-ethyl acetate 10:1 as an eluent to afford 174 mg of tert-butyl 2-cyano-6-methoxy-5-methyl-1H-indole-1-carboxylate.

To a stirred solution of 174 mg of tert-butyl 2-cyano-6-methoxy-5-methyl-1H-indole-carboxylate (0.61 mmol) in carbon tetrachloride (2.5 mL) was added 108 mg of N-bromosuccinimide (0.61 mmol) and 11 mg of AIBN (0.065 mmol). The mixture was refluxed for 1 h, then cooled and concentrated and filtered through short silica gel plug using hexane-ethyl acetate 10:1 to give 223 mg of crude tert-butyl 5-(bromomethyl)-2-cyano-6-methoxy-1H-indole-1-carboxylate that was used in the next step without further purification.

223 mg of ten-butyl 2-cyano-5-bromomethyl-1H-indole-1-carboxylate (0.61 mmol) and 193 mg of N-(piperidin-4-yl)-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-amine (0.61 mmol) were dissolved in 2 mL of DCM. 0.22 mL of DIPEA (0.2 mmol) was added to that solution and reaction mixture was stirred for 18 hs. Then reaction mixture was directly loaded on silica gel column and the product was eluted with DCM-MeOH 30:1. After evaporation of solvent boc-protected intermediate was dissolved in 0.5 mL of ACN and 0.06 mL of SnCl₄ (0.5 mmol) was added. The homogenous reaction mixture was stirred for 1 h and then all volatiles were removed in vacuo. The residue was quenched ammonia and extracted with ethyl acetate. Combined organic fractions were dried over MgSO₄ and concentrated. The residue was purified on silica gel column using hexane-ethyl acetate-MeOH 1:1:0.1 to produce 210 mg of 6-methoxy-5-((4-((6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl)amino)piperidin-1-yl)methyl)-1H-indole-2-carbonitrile (Compound 181). Its monohydrochloride salt was obtained by adding 1 equivalent of 1N HCl solution in diethyl ether to a solution of compound in ethanol. Monohydrochloride salt exists as a mixture of rotomers in approximate ratio 10:1, NMR is described for the major one: ¹H NMR (600 MHz, MeOD-d4): δ 8.71 (s, 1H), 7.87 (s, 1H), 7.86 (s, 1H), 7.24 (s, 1H), 7.12 (s, 1H), 4.66 (m, 1H), 4.49 (s, 2H), 4.03 (m, 5H), 3.69 (m, 2H), 3.34 (m, 2H), 2.36 (m, 2H), 2.18 (m, 2H). ¹³C NMR (150 MHz, MeOD-d4): δC 158.72, 149.70, 140.86, 133.08, 128.17, 127.75, 127.31, 123.36, 122.81, 121.69, 118.72, 115.07, 114.82, 114.60, 107.47, 94.60, 57.67, 56.62, 52.72, 35.22 (q, J=33 Hz), 29.53. ESI MS [MH¹]: 501.1675.

500 mg of 6-methoxy-5-((4-((6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl)amino)piperidin-1-yl)methyl)-1H-indole-2-carbonitrile (1 mmol) was slowly added to 5 mL of 1M BBr₃ in DCM at 0 degrees and reaction mixture was brought to RT. After 4 days ice was added to reaction mixture in the presence of sodium bicarbonate. Volatile organic was evaporated and the residue was partitioned between water and ethyl acetate-methanol 10:1. Organic layer was evaporated with silica gel and loaded on the column. The product was eluted with hexane-ethyl acetate-methanol 1:1:0.1, evaporation of fractions produced 300 mg of 6-hydroxy-5-((4-((6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl)amino)pipendin-1-yl)methyl)-1H-indole-2-carbonitrile (Compound 182). Its monohydrochloride salt was obtained by adding 1 equivalent of 1N HCl solution in diethyl ether to a solution of compound in ethanol. Monohydrochloride salt exists as a mixture of rotomers in approximate ratio 10:1, NMR is described for the major one: ¹H NMR (600 MHz, MeOD-d4): 8.70 (s, 1H), 7.81 (s, 1H), 7.77 (s, 1H), 7.21 (s, 1H), 6.98 (s, 1H), 4.64 (m, 1H), 4.48 (s, 1H), 4.01 (q, 2H, J=10.3 Hz), 3.66 (m, 2H), 3.35 (m, 2H), 2.37 (m, 2H), 2.12 (m, 2H). ¹³C NMR (150 MHz, MeOD-d4): δC 157.64, 156.62, 153.92, 141.09, 130.54, 127.75, 127.48, 125.65, 121.96, 121.59, 118.27, 115.23, 114.85, 113.98, 107.11, 97.45, 57.78, 52.88, 47.29, 35.54 (q, J=33 Hz), 29.95. ESI MS [MH⁺]: 487.1519.

Monohydrochloride salt exists as a mixture of rotomers in approximate ratio 10:1, NMR is described for the major one: ¹H NMR (600 MHz, MeOD-d4): 8.37 (s, 1H), 8.08 (s, 1H), 7.74 (d, 1H, J=8.8 Hz), 7.69 (s, 1H), 7.64 (d, 1H, J=8.8 Hz), 7.54 (s, 1H), 4.74 (m, 1H), 4.48 (m, 3H), 3.88 (q, 2H, J=10.6 Hz), 3.60 (m, 2H), 3.21 (m, 2H), 2.34 (m, 2H), 2.05 (m, 2H). ESI MS [MH⁺]: 514.1998.

331 mg of (R)-3-chloropropane-1,2-diol (3 mmol) and 530 mg of imidazole (7.8 mmol) were dissolved in 5 mL of dry dichloromethane. Then 7.2 mL of 1M TBDMSCl in dichloromethane was added. Reaction mixture was stirred overnight and then diluted with 20 mL of water. After separation the organic layer was dried over sodium sulfate and concentrated to produce 850 mg of (R)-5-(chloromethyl)-2,2,3,3,8,8,9,9-octamethyl-4,7-dioxa-3,8-disiladecane. The material was used as is in the next step.

To a solution of 39 mg of 5-methyl-1H-indole-2-carbonitrile (0.25 mmol) in 0.5 mL of DMF 15 mg of NaH (60% in oil, 0.375 mmol) was added and mixture was stirred for 30 min. Then 170 mg of (R)-5-(chloromethyl)-2,2,3,3,8,8,9,9-octamethyl-4,7-dioxa-3,8-disiladecane (0.5 mmol) was added and stirring continued for 24 hs. The reaction mixture was diluted with 10 mL of water and extracted with DCM. Combined organic extracts dried over sodium sulfate, concentrated and purified using silica gel column eluting with hexane-ethyl acetate 50:1 to afford 56 mg of (S)-1-(2,3-bis((tert-butyldimethylsilyl)oxy)propyl)-5-methyl-1H-indole-2-carbonitrile. ¹H NMR (600 MHz, CDCl3): δ 8.09 (d, 1H, J=8.8 Hz), 7.35 (s, 1H), 7.24 (d, 1H, J=8.8 Hz), 7.18 (s, 1H), 4.04 (m, 1H), 3.82 (m, 1H), 3.77 (m, 2H), 3.68 (m, 1H), 2.43 (s, 3H), 1.08 (m, 18H), 0.26 (m, 12H).

To a stirred solution of 55 mg of (S)-1-(2,3-bis((tert-butyldimethylsilyl)oxy)propyl)-5-methyl-1H-indole-2-carbonitrile (0.12 mmol) in carbon tetrachloride (0.5 mL) was added 21.3 mg of N-bromosuccinimide (0.12 mmol) and 1.1 mg of AIBN (0.0065 mmol). The mixture was refluxed for 1 h, then cooled, concentrated and filtered through short silica gel plug using hexane-ethyl acetate 10:1 to give 58 mg of crude (S)-1-(2,3-bis((ten-butyldimethyisilyl)oxy)propyl)-5-(bromomethyl)-1H-indole-2-carbonitrile that was used in the next step without further purification.

58 mg of (S)-1-(2,3-bis((tert-butyldimethylsilyl)oxy)propyl)-5-(bromomethyl)-1H-indole-2-carbonitrile (0.1 mmol) and 31 mg of N-(piperidin-4-yl)-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-amine (0.12 mmol) were dissolved in 0.2 mL of DCM. 26 mg of DIPEA (0.2 mmol) was added to that solution and reaction mixture was stirred for 18 hs. Then reaction mixture was directly loaded on silica gel column and the product was eluted with DCM-MeOH 30:1. After evaporation of solvent TBDMS-protected intermediate was dissolved in 0.2 mL of MeOH and 0.02 mL of 12M HCl was added. The homogenous reaction mixture was stirred overnight and then all volatiles were removed in vacuo. The residue was quenched ammonia and extracted with ethyl acetate. Combined organic fractions were dried over MgSO₄ and concentrated. The residue was purified on silica gel column using DCM-MeOH 20:1 to afford 15.9 mg of 5-((4-((6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl)amino)piperidin-1-yl)methyl)-1H-indole-2-carbonitrile (Compound 188). Its monohydrochloride salt was obtained by adding 1 equivalent of 1N HCl solution in diethyl ether to a solution of compound in ethanol. Monohydrochloride salt exists as a mixture of rotomers in approximate ratio 10:1, NMR is described for the major one: ¹H NMR (600 MHz, MeOD-d4): 8.63 (s, 1H), 7.95 (s, 1H), 7.78 (s, 1H), 7.77 (d, 1H, J=8.6 Hz), 7.63 (d, 1H, J=8.6 Hz), 7.37 (s, 1H), 4.57 (m, 1H), 4.56 (m, 1H), 4.50 (s, 2H) 4.37 (m, 1H), 4.04 (m, 1H), 3.99 (q, 2H, J=10.3 Hz), 3.65 (m, 2H), 3.60 (d, 2H, J=5.5 Hz), 3.29 (m, 2H), 2.37 (m, 2H), 2.12 (m, 2H). ¹³C NMR (150 MHz, MeOD-d4): δC 157.45, 150.99, 139.90, 132.27, 129.16127.89, 127.37, 127.00, 125.54, 123.11, 122.50, 118.58, 114.32, 114.25, 113.35, 113.31, 72.35, 64.85, 61.99, 52.44, 49.82, 48.12, 35.32 (q, J=33 Hz), 29.64. ESI MS [MH⁺]: 545.1941.

760 mg of 5-((4-((6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl)amino)piperidin-1-yl)methyl)-1H-indole-2-carbonitrile hydrochloride (1.5 mmol) and 207 mg of bromoacetamide (1.5 mmol) were dissolved in 3.6 mL of dry DMF. 1.96 g of cesium carbonate (6 mmol) was added and reaction mixture was stirred for 4 hs. Then it was quenched with 50 mL of water and extracted with DCM-MeOH 10:1. Combined organic extracts were evaporated with silica gel and loaded on column. The product was eluted with DCM-MeOH 10:1 mixture. After evaporation of product containing fractions it was recrystallized from MeOH to produce 319 mg of 2-(2-cyano-5-((4-((6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl)amino)piperidin-1-yl)methyl)-1H-indol-1-yl)acetamide, which was converted to hydrochloride salt by dissolving in 5 mL of MeOH, adding of 1eq of 1M HCl in water. Hydrochloride salt can be recrystallized further from MeOH. Monohydrochloride salt exists as a mixture of rotomers in approximate ratio 10:1, NMR is described for the major one: ¹H NMR (600 MHz, MeOD-d4): 8.44 (s, 1H), 7.91 (s, 1H), 7.57 (m, 2H), 7.41 (s, 1H), 5.10 (s, 2H), 4.53 (m, 1H), 4.47 (s, 1H), 3.89 (q, 2H, J=10.3 Hz), 3.62 (m, 2H), 3.24 (m, 2H), 2.35 (m, 2H), 1.93 (m, 2H). ¹³C NMR (150 MHz, MeOD-d4): δC 171.07, 157.66, 153.62, 140.17, 130.77, 129.55, 127.95, 127.10, 125.64, 123.46, 121.90, 118.31, 114.76, 113.69, 113.52, 112.60, 61.96, 52.67, 49.60, 47.98, 47.40, 35.52 (q, J=33 Hz), 29.96. ESI MS [MH⁺]: 528.1783.

Compound 219 was synthesized according following route:

Step 1: 30 g of 3-bromo-2-methylbenzoic acid (139 mmol) was dissolved in 180 mL of THF, cooled to 0 degrees and 9.5 g of lithium aluminium hydride (250 mmol) was added in small portions. After stirring for 3 hs no starting material was observed by TLC. Reaction mixture was carefully quenched with 20 mL of ethyl acetate and 20 mL of water. Silica gel was added and mixture was evaporated to dryness, loaded on small silica gel column. The product was eluted with hexane:ethyl acetate (1:1) resulting in 24 g of pure alcohol after evaporation. ¹H NMR (600 MHz, CDCl₃): 7.50 (d, 1H, J=8.1 Hz), 7.29 (d, 1H, J=8.1 Hz), 7.04 (t, 1H, J=8.1 Hz), 4.68 (s, 2H), 2.40 (s, 3H), 1.90 (br s, 1H). ¹³C NMR (150 MHz, CDCl₃): 140.60, 135.84, 132.03, 127.12, 126.70, 126.05.

Step 2: 24 g of (3-bromo-2-methylphenyl)methanol (119 mmol) was dissolved in 240 mL of dichloromethane and 103 g of manganese (IV) oxide (1.2 mol) was added. After stirring overnight TLC showed no starting material. Reaction mixture was evaporated with silica gel and loaded on small silica gel column. The product was eluted with hexane:ethyl acetate (10:1) to afford 18.6 g of pure aldehyde after evaporation. ¹H NMR (600 MHz, CDCl₃): 10.25 (s, 1H), 7.78 (m, 2H), 7.23 (t, 1H, J=7.7 Hz), 2.75 (s, 3H). ¹³C NMR (150 MHz, CDCl₃): 191.84, 137.72, 130.93, 130.20, 127.61, 127.37, 126.82, 18.13.

Step 3:

To the mixture of 18.6 g of 3-bromo-2-methylbenzaldehyde (93 mmol) and 26.8 g of methyl azidoacetate (233 mmol) in 130 mL of MeOH was added 43 mL of 5.4M MeONa over 30 minute at −10 degrees. After addition the mixture was stirred for additional hour at the same temperature and then transferred in cold room (4 degrees) and stirred overnight. On the morning reaction mixture was poured in 1 L mixture of ice and conc. ammonium chloride solution, stirred for 10 minutes and filtered off. The solid was washed with plenty of ice cold water and then moved at ambient temperature. After air drying for 1 hr the solid was dissolved in 100 mL of DCM, dried over magnesium sulfate and passed through short silica gel plug. Evaporation of solvent produced 21.1 g of methyl (E)-2-azido-3-(3-bromo-2-methylphenyl)acrylate, that was used in the next step without further purification. ¹H NMR (600 MHz, CDCl₃): 7.72 (d, 1H, J=7.7 Hz), 7.53 (d, 1H, J=7.7 Hz), 7.10 (s, 1H), 7.07 (t, 1H, J=7.7 Hz), 3.93 (s, 3H), 2.42 (s, 3H). ¹³C NMR (150 MHz, CDCl₃): 163.61, 136.65, 133.94, 133.09, 129.25, 128.76, 126.78, 125.81, 123.64, 53.10, 20.04.

Step 4:

21.1 g of methyl (E)-2-azido-3-(3-bromo-2-methylphenyl)acrylate (71 mmol) was dissolved in 700 mL of xylene. The mixture was refluxed for 10 minutes. Reaction mixture was cooled to RT and kept in −20 freezer overnight. The precipitated product was filtered off and dried on funnel to produce 10.0 g of methyl 5-bromo-4-methyl-1H-indole-2-carboxylate. ¹H NMR (600 MHz, CDCl₃): 8.98 (br s, 1H), 7.44 (d, 1H, J=8.4 Hz), 7.24 (s, 1H), 7.14 (d, 1H, J=8.4 Hz), 3.96 (s, 3H), 2.60 (s, 3H). ¹³C NMR (150 MHz, CDCl₃): 162.12, 135.38, 131.56, 129.52, 128.98, 127.36, 115.92, 110.82, 107.70, 52.15, 18.97.

Steps 5-7: 10.0 g of methyl 5-bromo-4-methyl-1H-indole-2-carboxylate (38 mmol) was refluxed in solution of 10.6 g KOH (190 mmol) in 130 mL of methanol for 1 hr. Reaction mixture was then concentrated and acidified with 12M HCl in water. Precipitated product was filtered off. After drying the 5-bromo-4-methyl-1H-indole-2-carboxylic acid was added to solution of 6.5 mL of oxalyl chloride (76 mmol) in 200 mL of dichloromethane with 0.6 mL of DMF. After stirring for 1 hr reaction mixture was cooled in ice-water bath and 40 mL of conc. ammonia in water was added dropwise. The heterogeneous mixture was stirred for another 3 hs and filtered off to obtain amide. A mixture of 5-bromo-4-methyl-1H-indole-2-carboxamide from previous step, 36 mL of phosphorus oxychloride (380 mmol) and 120 mL of chloroform was refluxed for 5 hs. Then reaction mixture was evaporated to dryness and quenched with ice and conc. ammonia (about 40 mL). The formed precipitate was filtered off, washed with plenty of water and dissolved in 100 mL of THF. The solution was evaporated with silica gel, loaded on medium silica gel column. The product was eluted hexane: ethyl acetate (2:1) affording 7.4 g of pure nitrile after evaporation. ¹H NMR (600 MHz, Me₂CO-d₆): 11.42 (br s, 1H), 7.49 (d, 1H, J=8.8 Hz), 7.42 (s, 1H), 7.32 (d, 1H, J=8.4 Hz), 2.59 (s, 3H). ¹³C NMR (150 MHz, Me₂CO-d₆): 137.48, 131.99, 130.95, 129.33, 117.21, 114.93, 113.71, 112.95, 108.51, 19.59.

Step 8: 2.35 g of 5-bromo-4-methyl-1H-indole-2-carbonitrile (10 mmol) was dissolved in 100 mL of THF, the flask was flushed with argon and 3.2 g of potassium hydride was added (30% suspension in oil, 24 mmol), after stirring for 5 minutes reaction mixture was cooled to −90 degrees (internal temperature, ethanol/N₂(liq.)) and 11.8 mL of tert-butyl lithium (20 mmol) was slowly added to maintain the temperature in the range −95-−90. After stirring for 1 hr 3.8 ml of DMF (50 mmol) was added dropwise and reaction mixture was allowed to warm to −70 degrees and kept 30 minutes at that temperature. The reaction mixture was quenched with 2.9 mL of acetic acid (50 mmol) and warmed to RT. After addition of 100 mL of brine organic phase was separated, evaporated with silica gel and loaded on medium silica gel column. Elution started with pure hexane and then product was washed out with hexane:THF (1:1). After evaporation of product containing fractions 1.11 g of pure aldehyde was obtained. ¹H NMR (600 MHz, CD₃CN): 10.39 (s, 1H), 7.82 (d, 1H, J=8.4 Hz), 7.51 (s, 1H), 7.43 (d, 1H, J=8.4 Hz), 2.86 (s, 3H). ¹³C NMR (150 MHz, CD₃CN): 191.15, 138.90, 137.17, 127.26, 126.94, 126.55, 113.70, 113.11, 109.97, 107.19, 13.39

Step 9: 800 mg of 5-formyl-4-methyl-1H-indole-2-carbonitrile (4.35 mmol), 1.83 g of N-(piperidin-4-yl)-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-amine hydrochloride (5.22 mmol) and 1.2 mL of triethylamine (8.7 mmol) were mixed in 43 mL of dry dichloromethane. 1.84 g of sodium triacetoxyborohydride (8.7 mmol) was added to it in one portion. After stirring overnight TLC showed absence of starting aldehyde in reaction mixture was transferred in separatory funnel and washed with 50 mL of 1M NaOH. Organic phase was evaporated with silica gel and loaded on silica gel column. The product was eluted starting from DCM:MeOH:NH₃*H₂O 40:1:0.1 to 15:1:0.1. Evaporation of solvent gave 2.08 g of oily product, which was dissolved in 5 mL of diethyl ether and crystallized upon standing. The product was filtered off, washed with additional 10 mL of ether and thoroughly dried to afford 1.95 g of white crystalline product (Compound 219, >99% purity HPLC). ¹H NMR (600 MHz, CDCl₃): 10.02 (br s, 1H), 8.46 (s, 1H), 7.31 (d, 1H, J=8.4 Hz), 7.24 (d, 1H, J=8.4 Hz), 7.22 (s, 1H), 7.16 (s, 1H), 5.53 (d, 1H, J=7.7 Hz), 4.22 (m, 1H), 3.64 (q, 2H, J=10.5 Hz), 3.60 (s, 2H), 2.90 (d, 2H, J=11.7 Hz), 2.56 (s, 3H), 2.25 (t, 2H, J=10.8 Hz), 2.07 (d, 2H, J=10.6 Hz), 1.57 (m, 2H). ¹³C NMR (150 MHz, CDCl₃): 166.75, 156.20, 154.39, 136.31, 130.67, 129.22, 127.71, 127.42, 123.86, 118.98, 116.57, 114.55, 112.79, 108.89, 105.94, 100.00, 60.35, 52.42, 48.16, 35.51 (q, J=32 Hz), 32.39, 15.12. HR MS (ESI): C₂₄H₂₃F₃N₆S+H⁺ calculated 485.1730. found 485.1732.

The compound was converted to hydrochloride salt by dissolving in 5 mL of MeOH, adding 4.4 mL of 1M HCl in water (4.4 mmol) and drying.

Step 1: 5 g of ethyl 1H-pyrazole-4-carboxylate (35.7 mmole) was dissolved in 70 mL of DMF, and 4.8 g of potassium tert-butoxide (42.8 mmol) was added. After stirring for 30 minutes 13.9 g of trityl chloride (50 mmol) was added in small portions. TLC indicated no starting material after 1 hr of stirring and reaction mixture was diluted with 300 ml of water and extracted with 3×50 ml of DCM. Organic extracts were evaporated and then dissolved in 300 mL of THF. 2.03 g of lithium aluminohydride (53.6 mmol) was added in small portions. After 1 hr reaction mixture was quenched with 10 mL of ethyl acetate following by 5 mL of water. 15 g of silica gel was added, mixture was evaporated and loaded on small silica gel column. The product was eluted with hexane-ethyl acetate 1:1 mixture. Evaporation of product containing fractions resulted in 11.75 g of (1-trityl-1H-pyrazol-4-yl)methanol.

Step 2: To a solution of 11.75 g of (1-trityl-1H-pyrazol-4-yl)methanol (34.5 mmol), 9.04 g triphenylphopshine (34.5 mmol) in 90 mL of DCM was added 6.14 g of N-Bromosuccinimide (34.5 mmol) at 0 degrees. Then mixture was stirred for 30 minutes and transferred in separatory funnel, washed with saturated sodium bicarbonate solution and brine, dried over sodium sulfate. After evaporation the residue was purified on conditioned silica gel column using hexane-ethyl acetate 10:1. Column conditioning (50 g of silica gel): washed with 500 mL of 0.05% of ammonia (conc. in water) in ethyl acetate, 500 mL of pure ethyl acetate and 500 mL of hexane. After evaporation of product containing fractions 11.09 g of 4-(bromomethyl)-1-trityl-1H-pyrazole was obtained, that was used in subsequent step immediately (decomposes on standing).

Step 3: 11.09 g of 4-(bromomethyl)-1-trityl-1H-pyrazole (27.5 mmol), 2.53 g 5-formyl-4-methyl-1H-indole-2-carbonitrile (13.8 mmol) and 13.6 g of cesium carbonate (41.4 mmol) were stirred in 28 mL of DMF for 30 minutes. Then reaction was diluted with 300 mL of water and 200 mL of diethyl ether. After stirring for 4 hs the precipitate was filtered off, washed with additional 100 ml of water and 100 mL of diethyl ether, dried to afford 16.4 g of 5-formyl-4-methyl-1-((1-trityl-1H-pyrazol-4-yl)methyl)-1H-indole-2-carbonitrile. ¹H NMR (600 MHz, DMSO-d6): 10.02 (s, 1H), 7.85 (s, 1H), 7.82 (d, 1H, J=8.4 Hz), 7.77 (d, 1H, J=8.4 Hz), 7.58 (s, 1H), 7.50 (s, 1H), 7.36 (m, 9H), 7.00 (m, 6H), 5.47 (s, 2H), 2.83 (s, 3H). ¹³C NMR (150 MHz, DMSO-d6): 191.13, 162.28, 142.67, 142.55, 138.52, 132.10, 129.66, 129.54, 127.85, 127.76, 127.14, 126.63, 115.56, 114.89, 109.77, 109.41, 78.46, 78.06, 14.12.

Step 4: 5.5 g of 5-formyl-4-methyl-1-((1-trityl-1H-pyrazol-4-yl)methyl)-1H-indole-2-carbonitrile (10.8 mmol) 5.8 g of N-(piperidin-4-yl)-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-amine hydrochloride (16.2 mmol) and 3 mL of triethylamine (21.6 mmol) were mixed in 110 mL of dry dichloromethane. 4.64 of sodium triacetoxyborohydride (21.6 mmol) was added to it in one portion. After stirring overnight TLC showed absence of starting aldehyde in reaction mixture was transferred in separatory funnel and washed with 100 mL of 1M NaOH. Organic phase was evaporated with silica gel and loaded on silica gel column. The product was eluted starting from DCM:MeOH:NH₃*H₂O 40:1:0.1 to 20:1:0.1. Evaporation of solvent gave 6.17 g of oily 4-methyl-5-((4-((6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl)amino)piperidin-1-yl)methyl)-1-((1-trityl-1H-pyrazol-4-yl)methyl)-1H-indole-2-carbonitrile. ¹H NMR (600 MHz, CDCl₃): 8.47 (s, 1H), 7.52 (s, 1H), 7.43 (s, 1H), 7.33 (d, 1H, J=8.4 Hz), 7.27 (m, 9H), 7.19 (s, 1H), 7.16 (d, 1H, J=8.4 Hz), 7.08 (m, 6H), 7.04 (s, 1H), 5.27 (s, 2H), 5.53 (d, 1H, J=7.7 Hz), 4.23 (m, 1H), 3.62 (q, 2H, J=10.5 Hz), 3.60 (s, 2H), 2.89 (m, 2H), 2.54 (s, 3H), 2.26 (t, 2H, J=10.6 Hz), 2.09 (d, 2H, J=10.3 Hz), 1.57 (d, 2H, J=9.9 Hz). ¹³C NMR (150 MHz, CDCl₃): 166.83, 156.03, 154.37, 142.89, 138.75, 136.42, 131.63, 131.24, 130.13, 130.08, 129.08, 127.81, 127.74, 127.43, 125.58, 118.35, 116.38, 115.40, 113.83, 112.35, 108.82, 107.36, 78.85, 60.21, 56.24, 52.32, 48.06, 39.90, 35.54 (q, J=32 Hz), 32.44, 15.03. HR MS (ESI): C₄₇H₄₁F₃N₈S+H⁺ calculated 807.3200. found 807.3197.

Step 5: 6.17 g of oily 4-methyl-5-((4-((6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl)amino)piperidin-1-yl)methyl)-1-((1-trityl-1H-pyrazol-4-yl)methyl)-1H-indole-2-carbonitrile was dissolved in 90 mL of ethyl acetate methanol 1:1 mixture. 6 mL of 4M HCl in dioxane was added. After stirring for 30 minutes the reaction mixture was concentrated and partitioned in DCM:MeOH 10:1 and saturated sodium carbonate solution. Organic phase was separated, evaporated with silica gel and loaded on silica gel column. Gradient elution with DCM:MeOH:NH₃*H₂O 50:1:0.1 to 7:1:0.1 and evaporation of product containing fractions resulted in 4.05 g of oil that crystallized upon standing. It was dissolved in 30 mL of methanol and 7 mL of 1M HCl. Evaporation and drying gave 3.7 g of hydrochloride of 1-((1H-pyrazol-4-yl)methyl)-4-methyl-5-((4-((6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl)amino)piperidin-1-yl)methyl)-1H-indole-2-carbonitrile (compound 309). Two rotamers are observed in NMR in approximate ratio 10:1. NMR is reported for the major rotamer. ¹H NMR (600 MHz, CD₃OD): 8.36 (s, 1H), 7.63 (m, 5H), 7.43 (s, 1H), 5.45 (s, 2H), 4.53 (s, 2H), 4.46 (m, 1H), 3.86 (q, 2H, J=10.5 Hz), 3.63 (m, 2H), 3.34 (m, 2H), 2.67 (s, 3H), 2.32 (m, 2H), 2.03 (m, 2H). ¹³C NMR (150 MHz, CD₃OD): 165.72, 157.61, 154.23, 138.70, 135.18, 130.91, 130.30, 128.73, 127.51, 125.68, 121.99, 121.12, 118.22, 114.39, 114.04, 111.04, 110.61, 58.83, 52.87, 47.25, 40.50, 35.61 (q, J=32 Hz), 29.90, 27.34, 15.89. HR MS (ESI): C₄₇H₄₁F₃N₈S+H⁺ calculated 807.3200. found 807.3197.

Step 1: 1 g of tert-butyl 4-(2-hydroxyethyl)piperazine-1-carboxylate (4.3 mmol) and 0.89 mL of triethyl amine (6.5 mmol) were dissolved in 14 mL of DCM. 0.4 mL of MsCl (5.2 mmol) was added slowly and reaction was stirred for 2 hs. After that it was washed with brine, dried over anhydrous sodium sulfate and evaporated. That intermediate was dissolved in 4 mL of DMF and 368 mg of 5-formyl-4-methyl-1H-indole-2-carbonitrile (2 mmol) and 2 g of cesium carbonate (6 mmol) were added. After stirring for 18 hs TLC showed consumption of aldehyde. The reaction mixture was diluted with 50 mL of water and extracted with 2×50 mL of DCM. Organics were evaporated with silica gel and loaded on silica gel column. The product was eluted with hexane-ethyl acetate 1:1 to afford 240 mg of tert-butyl 4-(2-(2-cyano-5-formyl-4-methyl-1H-indol-1-yl)ethyl)piperazine-1-carboxylate. HR MS (ESI): C₂₂H₂₈N₄O₃+H⁺ calculated 397.2234. found 397.2239.

Step 2: 120 mg of tert-butyl 4-(2-(2-cyano-5-formyl-4-methyl-1H-indol-1-yl)ethyl)piperazine-1-carboxylate (0.3 mmol) 126 mg of N-(piperidin-4-yl)-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-amine hydrochloride (0.36 mmol) and 0.06 mL of triethylamine (0.45 mmol) were mixed in 3 mL of dry dichloromethane. 97 mg of sodium triacetoxyborohydride (0.45 mmol) was added to it in one portion. After stirring overnight TLC showed absence of starting aldehyde in reaction mixture was transferred in separatory funnel and washed with 20 mL of 1M NaOH. Organic phase was evaporated with silica gel and loaded on silica gel column. The product was eluted starting from DCM:MeOH:NH₃*H₂O 40:1:0.1 to 20:1:0.1. Evaporation of solvent gave 180 mg of tert-butyl 4-(2-(2-cyano-4-methyl-5-((4-((6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl)amino)piperidin-1-yl)methyl)-1H-indol-1-yl)ethyl)piperazine-1-carboxylate. HR MS (ESI): C₃₅H₄₃F₃N₈O₂S+H⁺ calculated 697.3255. found 697.3259.

Step 3: 180 mg of tert-butyl 4-(2-(2-cyano-4-methyl-5-((4-((6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl)amino)piperidin-1-yl)methyl)-1H-indol-1-yl)ethyl)piperazine-1-carboxylate (0.26 mmol) was dissolved in 2.6 mL of ACN and 0.3 mL of SnCl₄ (2.6 mmol) was added. The homogenous reaction mixture was stirred for 1 h and then all volatiles were removed in vacuo. The residue was quenched ammonia and extracted with ethyl acetate. Combined organic fractions were dried over MgSO₄ and concentrated. The residue was purified using preparative TLC to afford 88 mg of 4-methyl-1-(2-(piperazin-1-yl)ethyl)-5-((4-((6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl)amino)piperidin-1-yl)methyl)-1H-indole-2-carbonitrile. ¹H NMR (600 MHz, CDCl₃): 8.46 (s, 1H), 7.35 (d, 1H, J=8.4 Hz), 7.17 (s, 1H), 7.15 (d, 1H, J=8.4 Hz), 7.10 (s, 1H), 5.20 (d, 1H, J=7.7 Hz), 4.32 (m, 2H), 4.22 (m, 1H), 3.63 (q, 2H, J=10.5 Hz), 3.60 (s, 2H), 2.91, (m, 6H), 2.69 (m, 2H), 2.54 (s, 3H), 2.50 (m, 4H), 2.26 (t, 2H, J=10.6 Hz), 2.09 (d, 2H, J=10.3 Hz), 1.58 (d, 2H, J=9.9 Hz). ¹³C NMR (150 MHz, CDCl₃): 166.79, 156.09, 154.36, 136.37, 131.18, 128.97, 128.65, 127.33, 125.61, 118.62, 116.43, 114.03, 111.64, 109.76, 107.23, 60.14, 57.80, 57.80, 53.86, 52.36, 51.34, 48.05, 45.48, 43.34, 35.53 (q, J=32 Hz), 32.39, 15.06. HR MS (ESI): C₃₀H₃₅F₃N₈S+H⁺ calculated 597.2730. found 597.2727.

Step 4: To a mixture of 20 mg of 4-methyl-1-(2-(piperazin-1-yl)ethyl)-5-((4-((6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl)amino)piperidin-1-yl)methyl)-1H-indole-2-carbonitrile (0.029 mmol) and 0.012 mL of DIPEA (0.069 mmol) in 0.3 mL of DCM was added 0.0028 mL of propionyl chloride (0.032 mmol). After stirring for 30 minutes reaction mixtures was loaded directly on pTLC and developed in DCM-MeOH 15:1. Washing silica gel and evaporating resulted in 19 mg of 4-methyl-1-(2-(4-propionylpiperazin-1-yl)ethyl)-5-((4-((6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl)amino)piperidin-1-yl)methyl)-1H-indole-2-carbonitrile (Compound 401). It was converted in hydrochloride by dissolving in 0.5 mL of methanol, adding 0.03 mL of 1M HCl in water and evaporating. ¹H NMR (600 MHz, CD₃OD): 8.35 (s, 1H), 7.61 (m, 2H), 7.54 (s, 1H), 7.48 (s, 1H), 4.60 (m, 2H), 4.55 (s, 2H), 3.86 (q, 2H, J=10.5 Hz), 3.61 (m, 4H), 3.35 (m, 2H), 2.98 (m, 2H), 2.70 (s, 3H), 2.70 (br, 2H), 2.39 (q, 2H, J=7.6 Hz), 2.35 (m, 2H), 1.99 (m, 2H), 1.10 (t, 3H, J=7.36 Hz). ¹³C NMR (150 MHz, CD₃OD): 174.85, 166.81, 157.98, 154.75, 138.82, 135.20, 130.79, 128.81, 127.53, 125.70, 121.77, 121.20, 118.19, 114.42, 112.33, 110.48, 58.85, 54.29, 53.99, 52.94, 47.12, 42.06, 35.63 (q, J=32 Hz), 29.98, 27.34, 27.14, 24.24, 15.81, 9.83. HR MS (ESI): C₃₃H₃₉F₃N₈OS+H⁺ calculated 653.2992. found 653.2988.

Monohydrochloride salt exists as a mixture of rotomers in approximate ratio 10:1, NMR is described for the major one: ¹H NMR (600 MHz, MeOD-d4): 8.56 (s, 1H), 7.94 (d, 1H, J=8.4 Hz), 7.89 (m, 2H), 7.70, (s, 1H), 7.46 (d, 1H, J=8.4 Hz), 4.60 (s, 2H), 4.54 (m, 1H), 3.93 (q, 2H, J=10.6 Hz), 3.67 (m, 2H), 3.28 (m, 2H), 2.35 (m, 2H), 2.04 (m, 2H). ¹³C NMR (150 MHz, MeOD-d4): δC 157.52, 151.57, 136.80, 134.03, 131.92, 127.24, 125.41, 124.16, 124.12, 122.23, 121.02, 120.49, 118.48, 118.12, 105.91, 104.66, 52.19, 52.06, 47.81, 35.43 (q, J=33 Hz), 29.73. ESI MS [MH⁺]: 471.1576.

Example 6 Representative Procedure for the Synthesis of Compounds from Subscaffold 5

Tert-butyl 4-((6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-ylamino)methyl) piperidine-1-carboxylate. To a solution of 4-chloro-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidine (50 mg, 0.20 mmol) in DMF (1 mL) was added N,N-diisopropylethylamine (52 □L, 0.30 mmol) and tert-butyl 4-(aminomethyl)piperidine-1-carboxylate (51 mg, 0.30 mmol). The solution was heated to 80° C. for 2 hours. The solution was diluted with EtOAc (10 mL) and washed with 10% NaHCO₃ (2×5 mL). The organic phase was dried Na₂SO₄ and evaporated in vacuo to give the product as a clear oil (103 mg, 80% yield) which was used without further purification. LC-MS: 2.49 min, 431.2 m/z [M+H]⁺, 375.1 m/z [M−t-Bu+H]⁺

6-(2,2,2-trifluoroethyl)-N-((piperidin-4-yl)methyl)thieno[2,3-d]pyrimidin-4-amine. Tert-butyl 4-((6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-ylamino)methyl) piperidine-1-carboxylate (103 mg, 0.24 mmol) was dissolved in TFA (1 mL). The solution was maintained at room temperature for 2 hours. The solution was then diluted with CHCl₃ (10 mL), and washed with 10% NaHCO₃ (2×5 mL). The organic phase was dried over Na₂SO₄ and evaporated in vacuo to give the product as a clear oil (56 mg, 85% yield). LC-MS: 1.48 min, 331.2 m/z [M+H]⁺.

To a vial containing 6-(2,2,2-trifluoroethyl)-N-((piperidin-4-yl)methyl)thieno[2,3-d]pyrimidin-4-amine (20 mg, 0.061 mmol) was added 1,2-dichloroethane (300 uL), 3-chloro-4-formylbenzene-1-sulfonamide (17 mg, 0.077 mmol), and sodium tri(acetoxy)borohydride (20 mg, 0.094 mmol). The mixture was stirred at room temperature for 4 hours. The mixture was diluted with EtOAc (5 mL), and washed with 0.1 N NaOH (2×1 mL). The volatiles were removed in vacuo. The resulting residue was purified by reversed-phase preparative HPLC (95:5-5:95 MeCN/H₂O with 0.1% TFA buffer). The product containing fractions were evaporated in vacuo to afford the product as a white solid (2.7 mg, 8.4% yield), Compound 253. LC-MS: 1.20 min, 534.1 m/z [M+H]⁺

Example 7 Representative Procedure for the Synthesis of Compounds from Subscaffold 3 and 4

5-(ethoxycarbonyl)-2-(2,2,2-trifluoroethyl)thieno[2,3-b]pyridin-4-yl trifluoromethanesulfonate. Ethyl 2-(2,2,2-trifluoroethyl)-4,5-dihydro-4-oxothieno[2,3-b]pyridine-5-carboxylate (91 mg, 0.30 mmol) (synthesized using similar procedure described in literature procedure J. Het. Chem. 1991, 28(8), 1953-5) was dissolved in dichloromethane (5 mL). N,N-diisopropylethylamine (157 uL, 0.90 mmol) was added. Solid N-phenyl-bis(trifluoromethanesulfonamide) (214 mg, 0.60 mmol) was added, and the mixture stirred for 10 minutes. The solution was washed with water (5 mL), dried over Na₂SO₄, and concentrated in vacuo to give an orange residue. Purification of the residue by silica gel chromatography (98:2 hexanes/EtOAc) afforded the product as a yellow solid (108 mg, 82% yield). LC-MS 3.22 min 438.2 m/z [M+H]⁺

Ethyl 4-(1-(tert-butoxycarbonyl)piperidin-4-ylamino)-2-(2,2,2-trifluoroethyl) thieno[2,3-b]pyridine-5-carboxylate. To a solution of 5-(ethoxycarbonyl)-2-(2,2,2-trifluoroethyl)thieno[2,3-b]pyridin-4-yl trifluoromethanesulfonate (108 mg, 0.25 mmol) in THF (2.5 mL) was added N,N-diisopropylethylamine (69 uL, 0.40 mmol) and tert-butyl 4-aminopiperidine-1-carboxylate (55 mg, 0.27 mmol). The solution was heated to 60° C. for 2 hours. The volatiles were removed in vacuo. The residue was dissolved in EtOAc (10 mL), washed subsequently with 0.1 N NaHSO₄ (2×5 mL) and saturated aq. NaHCO₃ (1×5 mL). The organic phase was dried over Na₂SO₄ and evaporated in vacuo to give the product as a white foam (122 mg), which was used without further purification. LC-MS: 2.73 min, 488.2 m/z [M+H]⁺, 432.1 m/z [M−t-Bu+H]⁺

Tert-butyl 4-(2-(2,2,2-trifluoroethyl)-5-(hydroxymethyl)thieno[2,3-b]pyridin-4-ylamino)piperidine-1-carboxylate. Ethyl 4-(1-(tert-butoxycarbonyl)piperidin-4-ylamino)-2-(2,2,2-trifluoroethyl) thieno[2,3-b]pyridine-5-carboxylate (122 mg, 0.25 mmol) was dissolved in THF (2.0 mL). Lithium borohydride (0.5 mL, 2.0 M solution in THF, 1.0 mmol) was added. The solution was heated to reflux under nitrogen for 1 hour. After cooling to room temperature, water (1 mL) was carefully added to the mixture. The mixture was concentrated in vacuo. Methanol (10 mL) was added and the solution concentrated to dryness on a rotary evaporator. The addition of methanol and evaporation was repeated three additional times. Purification of the resultant residue by silica gel chromatography (10:1 to 1:1 gradient of hexanes/EtOAc) afforded the product as a yellow solid (45 mg, 40% yield). LC-MS: 2.35 min, 446.3 m/z [M+H]⁺, 390.3 m/z [M−t-Bu+H]⁺

Ethyl 4-(1-(tert-butoxycarbonyl)piperidin-4-ylamino)-2-(2,2,2-trifluoroethyl)thieno[2,3-b]pyridine-5-carboxylate (45 mg, 0.1 mmol) was dissolved in CH₂Cl₂ (3 mL). Trifluoroacetic acid (2 mL) was added to the solution. After 2 hours, the solution was concentrated in vacuo. The residue was dissolved in CH₂Cl₂ (10 mL), and washed with a 10% solution of K₂CO₃ (2×1 mL), and dried over anhydrous K₂CO₃. The organic phase was concentrated to give tan residue, which was used in the next step without further purification. This residue was dissolved in 1,2-dichloroethane (1 mL). 5-formyl-1H-indole-2-carbonitrile (23 mg, 0.14 mmol) and sodium tri(acetoxy)borohydride (32 mg, 0.15 mmol) were added. The mixture was stirred at room temperature for 2 hours. The solution was diluted with EtOAc (10 mL) and washed with 0.1 N NaOH (1×5 mL). The organic phase was dried over Na₂SO₄ and concentrated in vacuo. The resulting residue was purified by reversed-phase preparative HPLC (95:5-5:95 MeCN/H₂O with 0.1% HCl buffer). The product containing fractions were lyophilized to afford the product as a white solid (1.4 mg, 2.5% yield), Compound 278. LC-MS: 1.45 min, 500.2 m/z [M+H]⁺.

Example 8 Fluorescence Polarization (FP) Assay

Fluorescence Polarization Assay.

Assays effective in monitoring the inhibition of the MLL binding to menin were developed during experiments performed during the development of embodiments of the present invention. A fluorescein-labeled 12-amino acid peptide derived from MLL containing the high affinity menin binding motif was produced (Yokoyama et al., Cell., 2005.123(2): p. 207-18, herein incorporated by reference in its entirety). Upon binding of the peptide (1.7 kDa) to the much larger menin (−67 kDa), the rotational correlation time of the fluorophore (peptide labeled with fluorescein at N-terminus) changes significantly, resulting in a substantial increase in the measured fluorescence polarization and fluorescence anisotropy (excitation at 500 nm, emission at 525 nm). The fluorescence polarization (FP) assay was utilized to determine the K_(d) for the binding of menin and the MLL peptide using a serial dilution of menin and 50 nM fluorescein-labeled MLL peptide. The titration curve demonstrates nanomolar affinity (K_(d)=56 nM) for the menin-MLL interaction.

The effectiveness of compounds (IC₅₀ values) in inhibiting the menin-MLL interaction was determined in the FP competition experiments. Compounds that inhibit the interaction decrease the fluorescence anisotropy which is being used as a read-out for compound screening and for IC₅₀ determination. For validation of the FP assay, a control competition experiment with unlabeled MLL peptide (no fluorescein attached) was performed. The competitive displacement of the fluorescein-labeled MLL peptide from menin by unlabeled MLL peptide was monitored. Using this assay, the IC₅₀ value for the MLL peptide with menin: IC₅₀=0.23 μM. In some embodiments of the present invention, the same competition FP assay is used for screening compounds targeting menin and inhibiting the menin-MLL interaction.

Biological activity of menin-MLL inhibitors is demonstrated in FIGS. 1-21. The IC₅₀ values shown in Tables 1-8 were measured using the above fluorescence polarization (FP) assay. 

The invention claimed is:
 1. A compound of Formula 4b:

or a pharmaceutically acceptable salt thereof, wherein each of R₁, R7, R₃, R₄, R₅, R₆, R₇, and R is independently H, alkyl, substituted alkyl, cycloalkyl, substituted cycloalkyl, alkene, alkyne, heteroalkyl, alcohol, diol, substituted diol, ether, amine, alkylamine, thiol, thioalkyl, halogen, carbocyclic ring, aryl, substituted aryl, heteroaryl, substituted heteroaryl, heterocycloalkyl, substituted heterocycloalkyl, aldehyde; ketone, CO—(CH₂)₁₋₆—H, CO-ethenyl, CO-propenyl, CO-ethynyl, CO-propynyl, CO—(CH₂)₁₋₆-aryl, CO—(CH₂)₁₋₆-heteroaryl, CO—(CH₂)₁₋₃-trifluoromethane, CO—(CH₂)₁₋₆-cycloalkane, carboxylic acid, alkylcarboxylic acid, ester, alkylester, amide, CO-amino-dialkyl, alkylamide; sulfoxide, sulfone, SO₂—(CH₂)₁₋₆—H, SO₂-alkenyl, SO₂-alkynyl, SO₂NH₂, SO₂—NH-alkyl, SO₂-amino-dialkyl, sulfinic acid, cyano, alkylcyano, methylcarbonitrile, cyanate, thiocyanate, azide, or phosphate; wherein R₆ is present at one or more positions of the indole; Y is N, C—H, or R^(a) is alkyl, substituted alkyl, Amy, cycloalkyl, heteroalkyl, alkyl-substituted aryl, substituted aryl, aromatic heterocycle, non-aromatic heterocycle, alcohol, ether, amine, cyano, sulfonyl, aldehyde, or aromatic group; L is alkylene, oxalkylene, or absent; wherein when L is absent the bonds attached to L do not exist; and each of E and G is independently N or C, wherein each of E and G is independently optionally substituted with R₆.
 2. The compound or pharmaceutically acceptable salt of claim 1, represented by the structure of Formula 4:


3. The compound or pharmaceutically acceptable salt of claim 1, represented by the structure of Formula 4c:

wherein X is a bond, alkylene, substituted alkylene, heteroalkylene, or substituted heteroalkylene; J is N, C—H, or C—R₁₂; M is N—R₉, O, S, SO₂, or C—(R₉)₂; each R₉ is independently H, alkyl, substituted alkyl, cycloalkyl, substituted cycloalkyl, alkene, alkyne, heteroalkyl, alcohol, diol, substituted diol, ether, amine, alkylamine, thiol, thioalkyl, halogen, carbocyclic ring, aryl, substituted aryl, heteroaryl, substituted heteroalkyl, heterocycloalkyl, substituted heterocycloalkyl, aldehyde, ketone, CO-alkyl, CO-alkenyl, CO-alkynyl, CO—(CH₂)₁₋₆-aryl, CO—(CH₂)₁₋₆-heteroaryl, CO—(CH₂)₁₋₃-trifluoromethane, CO—(CH₂)₁₋₆-cycloalkane, carboxylic acid, alkylcarboxylic acid, ester, alkylester, amide, CO-amino-dialkyl, alkylamide, sulfoxide, sulfone, SO₂—(CH₂)₁₋₆—H, SO₂-alkenyl, SO₂-alkynyl, SO₂NH₂, SO₂—NH— alkyl, SO₂-amino-dialkyl, sulfinic acid, cyano, alkylcyano, methylcarbonitrile, cyanate, thiocyanate, azide, or phosphate; R₁₀ is H, alkyl, substituted alkyl, cycloalkyl, substituted cycloalkyl, alkene, alkyne, heteroalkyl, alcohol, diol, substituted diol, ether, amine, alkylamine, thiol, thioalkyl, halogen, carbocyclic ring, aryl, substituted aryl, heteroaryl, substituted heteroaryl, heterocycloalkyl, substituted heterocycloalkyl, aldehyde, ketone, CO—(CH₂)₁₋₆—H, CO-ethenyl, CO-propenyl, CO-ethynyl, CO-propynyl, CO—(CH₂)₁₋₆-aryl, CO—(CH₂)₁₋₆-heteroaryl, CO—(CH₂)₁₋₃-trifluoromethane, CO—(CH₂)₁₋₆-cycloalkane, carboxylic acid, alkylcarboxylic acid, ester, alkylester, amide, CO-amino-dialkyl, alkylamide, sulfoxide, sulfone, SO₂—(CH₂)₁₋₆—H, SO₂-alkenyl, SO₂-alkynyl, SO₂NH₂, SO₂—NH-alkyl, SO₂-amino-dialkyl, sulfinic acid, ═O, cyano, alkylcyano, methylcarbonitrile, cyanate, thiocyanate, azide, or phosphate; and R₁₂ is alkyl, substituted alkyl, substituted alkyl, cycloalkyl, substituted cycloalkyl, hydroxyl, alcohol, amino, alkoxy, alkylamine, halogen, ketone, CO-alkyl, CO-alkenyl, CO-alkynyl, CO—(CH₂)₁₋₆-aryl, CO—(CH₂)₁₋₆-heteroaryl, CO—(CH₂)₁₋₃-trifluoromethane, CO—(CH₂)₁₋₆-cycloalkane, carboxylic acid, alkylcarboxylic acid, ester, alkylester, amide, alkylamide, cyano, alkylcyano, CONH₂, SO₂NH₂, SO₂-amino-dialkyl, SO₂—NH-alkyl, CO-amino-dialkyl, SO₂—(CH₂)₁₋₆—H, SO₂-alkenyl, SO₂-alkynyl, carbocyclic ring, aryl, substituted aryl, heteroaryl, or heterocycloalkyl.
 4. The compound or pharmaceutically acceptable salt of claim 3, wherein X is (CH₂)₀₋₆.
 5. The compound or pharmaceutically acceptable salt of claim 3, wherein X is alkylene or substituted alkylene.
 6. The compound or pharmaceutically acceptable salt of claim 3, wherein X is heteroalkylene or substituted heteroalkylene.
 7. The compound or pharmaceutically acceptable salt of claim 3, wherein J is N.
 8. The compound or pharmaceutically acceptable salt of claim 3, wherein M is N—R₉.
 9. The compound or pharmaceutically acceptable salt of claim 3, wherein R₉ is H, alkyl, substituted alkyl, alcohol, formyl, CO-alkyl, CO-alkenyl, CO-alkynyl, CO—(CH₂)₁₋₆-aryl, CO—(CH₂)₁₋₆-heteroaryl, CO—(CH₂)₁₋₃-trifluoromethane, CO—(CH₂)₁₋₆-cycloalkane, CONH₂, SO₂NH₂, SO₂-amino-dialkyl, SO₂—NH-alkyl, CO-amino-dialkyl, SO₂—(CH₂)₁₋₆—H, SO₂-alkenyl, or SO₂-alkynyl.
 10. The compound or pharmaceutically acceptable salt of claim 3, wherein R₁₀ is H, alkyl, ═O, trifluoromethane, or alcohol.
 11. The compound or pharmaceutically acceptable salt of claim 1, represented by the structure of Formula 4d:

wherein T is heteroaryl, cycloalkane, 5-membered ring comprising carbon atoms and one or more of N, S, and/or O; or 6-membered ring comprising carbon atoms and one or more of N, S, and/or O; wherein T is optionally substituted with R₁₁ at any position; and R₁₁ is H, alkyl, substituted alkyl, cycloalkyl, substituted cycloalkyl, alkene, alkyne, heteroalkyl, alcohol, diol, substituted diol, ether, amine, alkylarnine, thiol, thioalkyl, halogen, carbocyclic ring, aryl, substituted aryl, heteroaryl, substituted heteroaryl, heterocycloalkyl, substituted heterocycloalkyl, aldehyde, ketone, CO—(CH₂)₁₋₆—H, CO-ethenyl, CO-propenyl, CO-ethynyl, CO-propynyl, CO—(CH₂)₁₋₆-aryl, CO—(CH₂)₁₋₆-heteroaryl, CO—(CH₂)₁₋₃-trifluoromethane, CO—(CH₂)₁₋₆-cycloalkane, carboxylic add, alkylcarboxylic add, ester, alkylester, amide, CO-amino-dialkyl, alkylamide, sulfoxide, sulfone, SO₂—(CH₂)₁₋₆—H, SO₂-alkenyl, SO₂-alkynyl, SO₂NH₂, SO₂—NH-alkyl, SO₂-amino-dialkyl, sulfinic acid, cyano, alkylcyano, methylcarbonitrile, cyanate, thiocyanate, azide, or phosphate.
 12. The compound or pharmaceutically acceptable salt of claim 11, wherein T is cycloalkane.
 13. The compound or pharmaceutically acceptable salt of claim 12, wherein T comprises two or more rings that are fused, bridged, or spiro-connected.
 14. The compound or pharmaceutically acceptable salt of claim 11, wherein T is 5-membered ring comprising carbon atoms and one or more of N, S, and/or O or 6-membered ring comprising carbon atoms and one or more of N, S, and/or
 0. 15. The compound or pharmaceutically acceptable salt of claim 11, wherein R₁₁ is H, alkyl, substituted alkyl, alcohol, ether, amine, halogen, ketone, or amide.
 16. The compound or pharmaceutically acceptable salt of claim 11, wherein R₁₁ is H, alkyl, alcohol, O-alkyl, O—(CH₂)₁₋₃-cycloalkane, (CH₂)₁₋₃—O—(CH₂)₁₋₃—O-alkyl, (CH₂)₁₋₃—O—(CH₂)₁₋₃-cycloalkane, or (CH₂)₁₋₃-heteroaryl.
 17. The compound or pharmaceutically acceptable salt of claim 1, represented by the structure of Formula 7b:


18. The compound or pharmaceutically acceptable salt of claim 1, wherein Y is N.
 19. The compound or pharmaceutically acceptable salt of claim 18, wherein L is absent.
 20. The compound or pharmaceutically acceptable salt of claim 1, wherein R₁ is alkyl or substituted alkyl.
 21. The compound or pharmaceutically acceptable salt of claim 1, wherein R₁ is a halogen-substituted alkyl group.
 22. The compound or pharmaceutically acceptable salt of claim 1, wherein R₂ is H, alkyl, substituted alkyl, halogen, alcohol, ether, or amine.
 23. The compound or pharmaceutically acceptable salt of claim 1, wherein R₂ is H.
 24. The compound or pharmaceutically acceptable salt of claim 1, wherein R₃ is H, alkyl, amine, alcohol, heterocycloalkyl, or substituted alkyl.
 25. The compound or pharmaceutically acceptable salt of claim 1, wherein R₃ is H.
 26. The compound or pharmaceutically acceptable salt of claim 1, wherein R₄ is H, alkyl, substituted alkyl, alcohol, or amine.
 27. The compound or pharmaceutically acceptable salt of claim 1, wherein R₅ is H, alkyl, substituted alkyl, or alcohol.
 28. The compound or pharmaceutically acceptable salt of claim 1, wherein each R₆ is independently alkyl, substituted alkyl, alcohol, ether, halogen, amine, or cyano.
 29. The compound or pharmaceutically acceptable salt of claim 28, wherein each R₆ is independently alkyl, haloalkane, alcohol, ether, halogen, or amine.
 30. The compound or pharmaceutically acceptable salt of claim 28, comprising an R₆ connected to position 3, 4, or 6 of the indole.
 31. The compound or pharmaceutically acceptable salt of claim 28, comprising more than one R₆.
 32. The compound or pharmaceutically acceptable salt of claim 1, wherein R₇ is H, alkyl, substituted alkyl, alcohol, ether, heteroaryl, substituted heteroaryl, amide, or amine.
 33. The compound or pharmaceutically acceptable salt of claim 1, wherein R₇ is H, alkyl or substituted alkyl.
 34. The compound or pharmaceutically acceptable salt of claim 1, wherein R₇ is H, alkyl, haloalkane, alcohol, alkyl-SO₂-alkyl, alkyl-heterocycloalkyl, alkyl-heteroaryl, substituted alkyl-heteroaryl, (CH₂)_(n)—OR₁₃, (CH₂)_(n)R₁₃, (CH₂)_(n)—O—(CH₂)_(m)—R₁₃, (CH₂)₁₋₆—CO—NH₂, (CH₂)₁₋₆—CO-halogen, diol-substituted alkyl-R₁₄, diol-substituted heteroalkyl-R₁₄, heterocycloalkyl, substituted heterocycloalkyl, heteroaryl, or substituted heteroaryl, wherein n is 1-10; m is 1-10; R₁₃ is aryl, substituted aryl, heteroaryl, substituted heteroaryl, cycloalkyl, substituted cycloalkyl, heterocycloalkyl, or substituted heterocycloalkyl; and R₁₄ is amide, aryl, substituted aryl, heteroaryl, substituted heteroaryl, cycloalkyl, substituted cycloalkyl, heterocycloalkyl, or substituted heterocycloalkyl.
 35. The compound or pharmaceutically acceptable salt of claim 1, wherein R₇ is alkyl-heterocycloalkyl, alkyl-heteroaryl, or substituted alkyl-heteroaryl.
 36. The compound or pharmaceutically acceptable salt of claim 1, wherein R₇ is (CH₂)_(n)—OR₁₃, (CH₂)_(n)R₁₃, or (CH₂)_(n)—O—(CH₂)_(m)—R₁₃, wherein n is 1-10, m is 1-10, and R₁₃ is aryl, substituted aryl, heteroaryl, substituted heteroaryl, cycloalkyl, substituted cycloalkyl, heterocycloalkyl, or substituted heterocycloalkyl.
 37. The compound or pharmaceutically acceptable salt of claim 36, wherein the cycloalkyl or substituted cycloalkyl comprises two or more rings that are fused, bridged, or spiro-connected.
 38. The compound or pharmaceutically acceptable salt of claim 1, wherein R₈ is H, alkyl, substituted alkyl, alcohol, heteroaryl, substituted heteroaryl, cyano, amine, amide, sulfonylmethane, or ketone.
 39. The compound or pharmaceutically acceptable salt of claim 1, wherein R₈ is cyano.
 40. The compound or pharmaceutically acceptable salt of claim 1, wherein R₆, R₇, or R₈ is cyano, halo, alkyl, substituted alkyl, alcohol, heteroaryl, substituted heteroaryl, amine, amide, heterocycle, ether, or ketone.
 41. The compound or pharmaceutically acceptable salt of claim 1, wherein R_(a) is halo-substituted alkyl, (CH₂)—OH, (CH₂)_(n)—OR₁₅, amine, cyano, or aldehyde, wherein n is 0-10 and R₁₅ is alkyl, (CH₂)_(n)-aryl, (CH₂)_(n)-heterocycle, aryl, substituted aryl, heteroaryl, or heterocycle.
 42. The compound or pharmaceutically acceptable salt of claim 1, wherein L is absent.
 43. The compound or pharmaceutically acceptable salt of claim 1, wherein the compound is selected from:


44. A pharmaceutical composition comprising the compound or pharmaceutically acceptable salt of claim 1 and a pharmaceutically acceptable carrier.
 45. The pharmaceutical composition of claim 44, further comprising a second pharmaceutical agent.
 46. A method for the treatment of leukemia comprising administering the compound or pharmaceutically acceptable salt of claim 1 to a subject suffering from leukemia.
 47. The method of claim 46, wherein said leukemia comprises AML, ALL, or Mixed Lineage Leukemia.
 48. A method of inhibiting the interaction of menin and one or more of a MLL protein, a MLL fusion protein, and a MLL Partial Tandem Duplication comprising administering the compound or pharmaceutically acceptable salt of claim 1 to a sample comprising menin and one or more of the MLL protein, the MLL fusion protein, and the MLL Partial Tandem Duplication.
 49. The method of claim 48, wherein the MLL protein is MLL1 or MLL2.
 50. A method of treating a disorder mediated by menin interaction with another protein or by chromosomal rearrangement on chromosome 11q23, comprising administering to a subject in need thereof a therapeutically effective amount of the compound or pharmaceutically acceptable salt of claim
 1. 